/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with 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.*;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTabbedPane;
+import javax.swing.KeyStroke;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class GAlignFrame extends JInternalFrame
{
protected JMenu viewMenu = new JMenu();
+ protected JMenu annotationsMenu = new JMenu();
+
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
JMenuItem htmlMenuItem = new JMenuItem();
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+ public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
+ JMenuItem createGroup = new JMenuItem();
+
+ JMenuItem unGroup = new JMenuItem();
+
JMenuItem delete = new JMenuItem();
JMenuItem copy = new JMenuItem();
JMenuItem createPNG = new JMenuItem();
+ JMenuItem createBioJS = new JMenuItem();
+
+ JMenuItem createSVG = new JMenuItem();
+
protected JMenuItem font = new JMenuItem();
public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
JMenu jMenu2 = new JMenu();
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
protected ButtonGroup colours = new ButtonGroup();
protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenu cdna = new JMenu();
+
protected JMenuItem extractScores = new JMenuItem();
+ protected JMenuItem expandAlignment = new JMenuItem();
+
protected JMenu showProducts = new JMenu();
- public JMenuItem featureSettings = new JMenuItem();
+ public JMenuItem openFeatureSettings = new JMenuItem();
JMenuItem fetchSequence = new JMenuItem();
JMenuItem annotationColour = new JMenuItem();
+ JMenuItem annotationColumn = new JMenuItem();
+
+ protected JMenuItem rnahelicesColour = new JMenuItem();
+
JMenuItem associatedData = new JMenuItem();
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
+
JMenu addSequenceMenu = new JMenu();
JMenuItem addFromFile = new JMenuItem();
GridLayout gridLayout1 = new GridLayout();
JMenu jMenu3 = new JMenu();
-
+
JMenuItem showAllSeqs = new JMenuItem();
JMenuItem showAllColumns = new JMenuItem();
JMenuItem hideSelColumns = new JMenuItem();
+ JMenuItem hideAllButSelection = new JMenuItem();
+
+ JMenuItem hideAllSelection = new JMenuItem();
+
+ JMenuItem showAllhidden = new JMenuItem();
+
+ protected JMenuItem showAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem showAllAlAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllAlAnnotations = new JMenuItem();
+
+ protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
JMenuItem invertColSel = new JMenuItem();
JMenuItem textColour = new JMenuItem();
- JMenu formatMenu = new JMenu();
+ protected JMenu formatMenu = new JMenu();
JMenu selectMenu = new JMenu();
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();
-
+
JMenu tooltipSettingsMenu = new JMenu();
- private JMenuItem justifyLeftMenuItem=new JMenuItem();
+ private JMenuItem justifyLeftMenuItem = new JMenuItem();
- private JMenuItem justifyRightMenuItem=new JMenuItem();
+ private JMenuItem justifyRightMenuItem = new JMenuItem();
JMenu autoAnnMenu = new JMenu();
- protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showConsensusProfile=new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
+
+ 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 JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
private JMenuItem grpsFromSelection = new JMenuItem();
+
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ private boolean showAutoCalculatedAbove = false;
+
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+
public GAlignFrame()
{
try
JMenuItem item = new JMenuItem(
jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
}
} catch (Exception e)
{
+ System.err.println(e.toString());
}
if (!new jalview.util.Platform().isAMac())
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
|| SwingUtilities.isRightMouseButton(evt))
{
- radioItem
- .removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(nucleotideColour);
-
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
+ colours.add(tcoffeeColour);
+ colours.add(RNAInteractionColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
switch (index)
{
- case ColourSchemeProperty.NONE:
- noColourmenuItem.setSelected(true);
- break;
case ColourSchemeProperty.CLUSTAL:
clustalColour.setSelected(true);
break;
+ case ColourSchemeProperty.TCOFFEE:
+ tcoffeeColour.setSelected(true);
+ break;
+
+ case ColourSchemeProperty.PURINEPYRIMIDINE:
+ purinePyrimidineColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
+ /*
+ * case ColourSchemeProperty.COVARIATION:
+ * covariationColour.setSelected(true);
+ *
+ * break;
+ */
case ColourSchemeProperty.USER_DEFINED:
userDefinedColour.setSelected(true);
break;
+ case ColourSchemeProperty.NONE:
+ default:
+ noColourmenuItem.setSelected(true);
+ break;
+
}
}
private void jbInit() throws Exception
{
- fileMenu.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()
+ fileMenu.setText(MessageManager.getString("action.file"));
+
+ saveAs.setText(MessageManager.getString("action.save_as") + "...");
+ ActionListener al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
saveAs_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()
+ };
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ addMenuActionAndAccelerator(keyStroke, saveAs, al);
+
+ closeMenuItem.setText(MessageManager.getString("action.close"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
closeMenuItem_actionPerformed(false);
}
- });
- 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()
- {
- public void actionPerformed(ActionEvent e)
- {
- selectAllSequenceMenuItem_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()
- {
- public void actionPerformed(ActionEvent e)
- {
- deselectAllSequenceMenuItem_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()
- {
- public void actionPerformed(ActionEvent e)
- {
- invertSequenceMenuItem_actionPerformed(e);
- }
- });
- grpsFromSelection.setText("Make Groups for selection");
- grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
+
+ editMenu.setText(MessageManager.getString("action.edit"));
+ viewMenu.setText(MessageManager.getString("action.view"));
+ annotationsMenu.setText(MessageManager.getString("action.annotations"));
+ colourMenu.setText(MessageManager.getString("action.colour"));
+ calculateMenu.setText(MessageManager.getString("action.calculate"));
+ webService.setText(MessageManager.getString("action.web_service"));
+
+ selectAllSequenceMenuItem.setText(MessageManager
+ .getString("action.select_all"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ selectAllSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
+
+ deselectAllSequenceMenuItem.setText(MessageManager
+ .getString("action.deselect_all"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
+
+ invertSequenceMenuItem.setText(MessageManager
+ .getString("action.invert_sequence_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ invertSequenceMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
+ grpsFromSelection.setText(MessageManager
+ .getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(new ActionListener()
+ {
+ @Override
public void actionPerformed(ActionEvent e)
{
makeGrpsFromSelection_actionPerformed(e);
- }
+ }
});
+ expandAlignment.setText(MessageManager
+ .getString("action.view_flanking_regions"));
+ expandAlignment.setToolTipText(MessageManager
+ .getString("label.view_flanking_regions"));
+ expandAlignment.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ expand_newalign(e);
+ }
+ });
+ remove2LeftMenuItem.setText(MessageManager
+ .getString("action.remove_left"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2LeftMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
- 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()
- {
- 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()
- {
- 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()
- {
- 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()
- {
- public void actionPerformed(ActionEvent e)
- {
- removeAllGapsMenuItem_actionPerformed(e);
- }
- });
- justifyLeftMenuItem.setText("Left Justify Alignment");
- justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+ remove2RightMenuItem.setText(MessageManager
+ .getString("action.remove_right"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
- public void actionPerformed(ActionEvent e)
- {
- justifyLeftMenuItem_actionPerformed(e);
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2RightMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
+
+ removeGappedColumnMenuItem.setText(MessageManager
+ .getString("action.remove_empty_columns"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeGappedColumnMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
+
+ removeAllGapsMenuItem.setText(MessageManager
+ .getString("action.remove_all_gaps"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeAllGapsMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
+ justifyLeftMenuItem.setText(MessageManager
+ .getString("action.left_justify_alignment"));
+ justifyLeftMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
});
- justifyRightMenuItem.setText("Right Justify Alignment");
- justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
+ justifyRightMenuItem.setText(MessageManager
+ .getString("action.right_justify_alignment"));
+ justifyRightMenuItem.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e)
- {
- justifyRightMenuItem_actionPerformed(e);
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyRightMenuItem_actionPerformed(e);
+ }
});
- viewBoxesMenuItem.setText("Boxes");
+ viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewBoxesMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewBoxesMenuItem_actionPerformed(e);
}
});
- viewTextMenuItem.setText("Text");
+ viewTextMenuItem.setText(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewTextMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewTextMenuItem_actionPerformed(e);
}
});
- showUnconservedMenuItem.setText("Show Unconserved");
- showUnconservedMenuItem.setState(false);
- showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showNonconservedMenuItem.setText(MessageManager
+ .getString("label.show_non_conversed"));
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showUnconservedMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("by Pairwise Identity");
- sortPairwiseMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sortPairwiseMenuItem_actionPerformed(e);
- }
- });
- sortIDMenuItem.setText("by ID");
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ sortPairwiseMenuItem.setText(MessageManager
+ .getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortPairwiseMenuItem_actionPerformed(e);
+ }
+ });
+ sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortIDMenuItem_actionPerformed(e);
}
});
- sortLengthMenuItem.setText("By Length");
- sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
+ sortLengthMenuItem
+ .setText(MessageManager.getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortLengthMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("by Group");
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortGroupMenuItem_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()
- {
- public void actionPerformed(ActionEvent e)
- {
- removeRedundancyMenuItem_actionPerformed(e);
- }
- });
- pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
- pairwiseAlignmentMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- pairwiseAlignmentMenuItem_actionPerformed(e);
- }
- });
- PCAMenuItem.setText("Principal Component Analysis");
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ removeRedundancyMenuItem.setText(MessageManager.getString(
+ "action.remove_redundancy").concat("..."));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+ pairwiseAlignmentMenuItem.setText(MessageManager
+ .getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed(e);
+ }
+ });
+ PCAMenuItem.setText(MessageManager
+ .getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
public void actionPerformed(ActionEvent e)
{
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem
- .setText("Average Distance Using % Identity");
- averageDistanceTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
- neighbourTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- neighbourTreeMenuItem_actionPerformed(e);
- }
- });
+ averageDistanceTreeMenuItem.setText(MessageManager
+ .getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ averageDistanceTreeMenuItem_actionPerformed(e);
+ }
+ });
+ neighbourTreeMenuItem.setText(MessageManager
+ .getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ neighbourTreeMenuItem_actionPerformed(e);
+ }
+ });
this.getContentPane().setLayout(borderLayout1);
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.setText(MessageManager.getString("label.clustalx"));
- clustalColour.addActionListener(new java.awt.event.ActionListener()
+ clustalColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed(e);
}
});
- zappoColour.setText("Zappo");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
+ zappoColour.setText(MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed(e);
}
});
- taylorColour.setText("Taylor");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
+ taylorColour.setText(MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
- helixColour.setText("Helix Propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
+ hydrophobicityColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed(e);
}
});
- strandColour.setText("Strand Propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
+ strandColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed(e);
}
});
- turnColour.setText("Turn Propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
+ turnColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed(e);
}
});
- buriedColour.setText("Buried Index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
+ buriedColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText("User Defined...");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
+ userDefinedColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText("BLOSUM62 Score");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ BLOSUM62Colour
+ .setText(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed(e);
}
});
- avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
- njTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
+ /*
+ * covariationColour.setText("Covariation");
+ * covariationColour.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
+ * });
+ */
+
+ avDistanceTreeBlosumMenuItem.setText(MessageManager
+ .getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ avTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ njTreeBlosumMenuItem.setText(MessageManager
+ .getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText("Show Annotations");
- annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
- "SHOW_ANNOTATIONS", true));
- annotationPanelMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotationPanelMenuItem_actionPerformed(e);
- }
- });
- colourTextMenuItem.setText("Colour Text");
- colourTextMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- colourTextMenuItem_actionPerformed(e);
- }
- });
- htmlMenuItem.setText("HTML");
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ annotationPanelMenuItem.setText(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
+ true));
+ annotationPanelMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationPanelMenuItem_actionPerformed(e);
+ }
+ });
+ 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)
+ {
+ showAllAnnotations_actionPerformed(false, true);
+ }
+ });
+ hideAllAlAnnotations.setText(MessageManager
+ .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllAlAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllAnnotations_actionPerformed(false, true);
+ }
+ });
+ showAllSeqAnnotations.setText(MessageManager
+ .getString("label.show_all_seq_annotations"));
+ showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllSeqAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllAnnotations_actionPerformed(true, false);
+ }
+ });
+ hideAllSeqAnnotations.setText(MessageManager
+ .getString("label.hide_all_seq_annotations"));
+ hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllSeqAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllAnnotations_actionPerformed(true, false);
+ }
+ });
+ SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBySequence.setText(MessageManager
+ .getString("label.sort_annotations_by_sequence"));
+ sortAnnBySequence
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ sortAnnBySequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
+ }
+ });
+ sortAnnByLabel.setText(MessageManager
+ .getString("label.sort_annotations_by_label"));
+ sortAnnByLabel
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
+ }
+ });
+ colourTextMenuItem.setText(MessageManager
+ .getString("label.colour_text"));
+ colourTextMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ colourTextMenuItem_actionPerformed(e);
+ }
+ });
+ htmlMenuItem.setText(MessageManager.getString("label.html"));
+ htmlMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview Window");
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ // TODO uncomment when supported by MassageManager
+ // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
+ createBioJS.setText("BioJS");
+ createBioJS.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ bioJSMenuItem_actionPerformed(e);
+ }
+ });
+
+ overviewMenuItem.setText(MessageManager
+ .getString("label.overview_window"));
+ overviewMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
overviewMenuItem_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()
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
undoMenuItem_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
+
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()
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
redoMenuItem_actionPerformed(e);
}
+ };
+ addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
});
- conservationMenuItem.setText("By Conservation");
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
- noColourmenuItem.setText("None");
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed(e);
}
});
- wrapMenuItem.setText("Wrap");
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ wrapMenuItem.setText(MessageManager.getString("label.wrap"));
+ wrapMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
wrapMenuItem_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()
+
+ printMenuItem.setText(MessageManager.getString("action.print") + "...");
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
printMenuItem_actionPerformed(e);
}
- });
- renderGapsMenuItem.setText("Show Gaps");
- renderGapsMenuItem.setState(true);
+ };
+ addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
+
renderGapsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- renderGapsMenuItem_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()
+ .setText(MessageManager.getString("action.show_gaps"));
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- findMenuItem_actionPerformed(e);
+ renderGapsMenuItem_actionPerformed(e);
}
});
- abovePIDThreshold.setText("Above Identity Threshold");
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+
+ findMenuItem.setText(MessageManager.getString("action.find"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.find_tip")));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ findMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+
+ abovePIDThreshold.setText(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
abovePIDThreshold_actionPerformed(e);
}
});
- showSeqFeatures.setText("Show Sequence Features");
+ showSeqFeatures.setText(MessageManager
+ .getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
showSeqFeatures_actionPerformed(actionEvent);
}
});
-/*
- * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
- showSeqFeaturesHeight.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- showSeqFeaturesHeight_actionPerformed(actionEvent);
- }
- }); */
- showDbRefsMenuitem.setText("Show Database Refs");
+ /*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+ * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
+ * void actionPerformed(ActionEvent actionEvent) {
+ * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
+ */
+ showDbRefsMenuitem.setText(MessageManager
+ .getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
}
-
+
});
- showNpFeatsMenuitem.setText("Show Non-Positional Features");
+ showNpFeatsMenuitem.setText(MessageManager
+ .getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
}
-
+
});
- showGroupConservation.setText("Group Conservation");
+ showGroupConservation.setText(MessageManager
+ .getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
}
-
+
});
- showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.setText(MessageManager
+ .getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
}
-
+
});
- showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.setText(MessageManager
+ .getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
}
-
+
+ });
+ showSequenceLogo.setText(MessageManager
+ .getString("label.show_consensus_logo"));
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
});
- showConsensusProfile.setText("Show Consensus Logo");
- showConsensusProfile.addActionListener(new ActionListener()
+ normaliseSequenceLogo.setText(MessageManager
+ .getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- showConsensusProfile_actionPerformed(e);
+ normaliseSequenceLogo_actionPerformed(e);
}
-
+
});
- applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setText(MessageManager
+ .getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
-
+ @Override
public void actionPerformed(ActionEvent e)
{
applyAutoAnnotationSettings_actionPerformed(e);
}
-
});
- nucleotideColour.setText("Nucleotide");
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ ButtonGroup buttonGroup = new ButtonGroup();
+ buttonGroup.add(showAutoFirst);
+ buttonGroup.add(showAutoLast);
+ showAutoFirst.setText(MessageManager.getString("label.show_first"));
+ showAutoFirst.setSelected(Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false));
+ showAutoFirst.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+ showAutoLast.setText(MessageManager.getString("label.show_last"));
+ showAutoLast.setSelected(!showAutoFirst.isSelected());
+ showAutoLast.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideColour_actionPerformed(e);
}
});
- 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()
+
+ tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ tcoffeeColorScheme_actionPerformed(e);
+ }
+ });
+
+ deleteGroups
+ .setText(MessageManager.getString("action.undefine_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteGroups_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
+ createGroup.setText(MessageManager.getString("action.create_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroup_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
+ unGroup.setText(MessageManager.getString("action.remove_group"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- deleteGroups_actionPerformed(e);
+ unGroup_actionPerformed(e);
}
- });
- copy.setText("Copy");
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ };
+ addMenuActionAndAccelerator(keyStroke, unGroup, al);
- copy.addActionListener(new java.awt.event.ActionListener()
+ copy.setText(MessageManager.getString("action.copy"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed(e);
}
- });
- 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()
+ };
+ addMenuActionAndAccelerator(keyStroke, copy, al);
+
+ cut.setText(MessageManager.getString("action.cut"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed(e);
}
- });
- 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, cut, al);
+
+ delete.setText(MessageManager.getString("action.delete"));
+ delete.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
delete_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()
+
+ pasteMenu.setText(MessageManager.getString("action.paste"));
+ pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteNew_actionPerformed(e);
}
- });
- 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, pasteNew, al);
+
+ pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteThis_actionPerformed(e);
}
- });
- applyToAllGroups.setText("Apply Colour To All Groups");
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
+ applyToAllGroups.setText(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
applyToAllGroups_actionPerformed(e);
}
});
- createPNG.addActionListener(new java.awt.event.ActionListener()
+ createPNG.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createPNG(null);
}
});
- createPNG.setActionCommand("Save As PNG Image");
+ createPNG.setActionCommand(MessageManager
+ .getString("label.save_png_image"));
createPNG.setText("PNG");
- font.setText("Font...");
- font.addActionListener(new java.awt.event.ActionListener()
+
+ font.setText(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()
+ 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()
+
+ createSVG.setText("SVG");
+ createSVG.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSVG(null);
+ }
+ });
+
+ LoadtreeMenuItem.setActionCommand(MessageManager
+ .getString("label.load_tree_for_sequence_set"));
+ LoadtreeMenuItem.setText(MessageManager
+ .getString("label.load_associated_tree"));
+ 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);
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText("Centre Column Labels");
- centreColumnLabelsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- centreColumnLabels_actionPerformed(e);
- }
- });
+ centreColumnLabelsMenuItem.setText(MessageManager
+ .getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ centreColumnLabels_actionPerformed(e);
+ }
+ });
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText("Automatic Scrolling");
+ followHighlightMenuItem.setText(MessageManager
+ .getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
followHighlight_actionPerformed();
}
-
+
});
-
- modifyPID.setText("Modify Identity Threshold...");
- modifyPID.addActionListener(new java.awt.event.ActionListener()
+
+ modifyPID.setText(MessageManager
+ .getString("label.modify_identity_thereshold"));
+ modifyPID.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
modifyPID_actionPerformed(e);
}
});
- modifyConservation.setText("Modify Conservation Threshold...");
- modifyConservation
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- modifyConservation_actionPerformed(e);
- }
- });
- sortByTreeMenu.setText("By Tree Order");
- sort.setText("Sort");
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_thereshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed(e);
+ }
+ });
+ sortByTreeMenu
+ .setText(MessageManager.getString("action.by_tree_order"));
+ sort.setText(MessageManager.getString("action.sort"));
sort.addMenuListener(new MenuListener()
{
+ @Override
public void menuSelected(MenuEvent e)
{
buildTreeMenu();
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuCanceled(MenuEvent e)
{
}
});
- sortByAnnotScore.setText("by Score");
+ sortByAnnotScore.setText(MessageManager
+ .getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
- sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+ sort.addMenuListener(new javax.swing.event.MenuListener()
{
+ @Override
public void menuCanceled(MenuEvent e)
{
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuSelected(MenuEvent e)
{
buildSortByAnnotationScoresMenu();
});
sortByAnnotScore.setVisible(false);
- calculateTree.setText("Calculate Tree");
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree"));
- jMenu2.setText("Export Image");
- padGapsMenuitem.setText("Pad Gaps");
+ jMenu2.setText(MessageManager.getString("label.export_image"));
+ 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);
}
});
vamsasStore.setVisible(false);
- vamsasStore.setText("VAMSAS store");
+ vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
vamsasStore.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText("Translate cDNA");
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showTranslation_actionPerformed(e);
}
});
- extractScores.setText("Extract Scores...");
+
+ /*
+ * cDNA menu options
+ */
+ cdna.setText(MessageManager.getString("label.cdna"));
+ // link to available cDNA
+ JMenuItem linkCdna = new JMenuItem(
+ MessageManager.getString("label.link_cdna"));
+ linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.link_cdna_tip")));
+ linkCdna.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ linkCdna_actionPerformed();
+ }
+ });
+ cdna.add(linkCdna);
+ // align linked cDNA
+ JMenuItem alignCdna = new JMenuItem(
+ MessageManager.getString("label.align_cdna"));
+ alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.align_cdna_tip")));
+ alignCdna.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ alignCdna_actionPerformed();
+ }
+ });
+ cdna.add(alignCdna);
+
+ // view alignment as cDNA (when known)
+ JMenuItem viewAsCdna = new JMenuItem(
+ MessageManager.getString("label.view_as_cdna"));
+ viewAsCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.view_as_cdna_tip")));
+ viewAsCdna.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ viewAsCdna_actionPerformed();
+ }
+ });
+ cdna.add(viewAsCdna);
+
+ extractScores.setText(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() {
- *
- * public void actionPerformed(ActionEvent e) {
- * showProducts_actionPerformed(e); } });
- */
- featureSettings.setText("Feature Settings...");
- featureSettings.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"));
+ openFeatureSettings.setText(MessageManager
+ .getString("label.feature_settings"));
+ openFeatureSettings.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
featureSettings_actionPerformed(e);
}
});
- fetchSequence.setText("Fetch Sequence(s)...");
+ fetchSequence
+ .setText(MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fetchSequence_actionPerformed(e);
}
});
- annotationColour.setText("By Annotation...");
+ annotationColour.setText(MessageManager
+ .getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotationColour_actionPerformed(e);
}
});
- associatedData.setText("Load Features / Annotations");
+
+ annotationColumn.setText(MessageManager
+ .getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColumn_actionPerformed(e);
+ }
+ });
+
+ rnahelicesColour.setText(MessageManager
+ .getString("action.by_rna_helixes"));
+ rnahelicesColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ rnahelicesColour_actionPerformed(e);
+ }
+ });
+
+ associatedData.setText(MessageManager
+ .getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
associatedData_actionPerformed(e);
}
});
- autoCalculate.setText("Autocalculate Consensus");
+ 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);
+ }
+ });
+
+ addSequenceMenu
+ .setText(MessageManager.getString("label.add_sequences"));
+ addFromFile.setText(MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromFile_actionPerformed(e);
}
});
- addFromText.setText("From Textbox");
+ addFromText.setText(MessageManager.getString("label.from_textbox"));
addFromText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromText_actionPerformed(e);
}
});
- addFromURL.setText("From URL");
+ addFromURL.setText(MessageManager.getString("label.from_url"));
addFromURL.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText("Export Features...");
+ exportFeatures.setText(MessageManager
+ .getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText("Export Annotations...");
+ exportAnnotations.setText(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");
+ jMenu3.setText(MessageManager.getString("action.show"));
+ showAllSeqs.setText(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");
+ showAllColumns.setText(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");
+ hideMenu.setText(MessageManager.getString("action.hide"));
+ hideSelSequences.setText(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");
+ hideSelColumns.setText(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");
+ hideAllSelection.setText(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.
+ hideAllButSelection.setText(MessageManager
+ .getString("label.all_but_selected_region"));
+ hideAllButSelection.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllButSelection_actionPerformed(e);
+ }
+ });
+ showAllhidden.setText(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()
+
+ invertColSel.setText(MessageManager
+ .getString("action.invert_column_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
invertColSel_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
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);
});
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()
+
+ save.setText(MessageManager.getString("action.save"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
save_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, save, al);
+
reload.setEnabled(false);
- reload.setText("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()
+
+ newView.setText(MessageManager.getString("action.new_view"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
newView_actionPerformed(e);
}
- });
- tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
- + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
- textColour.setText("Colour Text ...");
+ };
+ addMenuActionAndAccelerator(keyStroke, newView, al);
+
+ tabbedPane.setToolTipText("<html><i>"
+ + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ + "</i></html>");
+ textColour.setText(MessageManager.getString("label.colour_text")
+ + "...");
textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed(e);
}
});
- formatMenu.setText("Format");
- selectMenu.setText("Select");
- idRightAlign.setText("Right Align Sequence Id");
+ formatMenu.setText(MessageManager.getString("action.format"));
+ selectMenu.setText(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);
+
+ pageSetup
+ .setText(MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText("Alignment Properties...");
+ alignmentProperties.setText(MessageManager
+ .getString("label.alignment_props") + "...");
alignmentProperties.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
alignmentProperties();
}
});
- tooltipSettingsMenu.setText("Sequence ID Tooltip");
- autoAnnMenu.setText("Autocalculated Annotation");
+ tooltipSettingsMenu.setText(MessageManager
+ .getString("label.sequence_id_tooltip"));
+ autoAnnMenu.setText(MessageManager
+ .getString("label.autocalculated_annotation"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(annotationsMenu);
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
// dont add these yet in the CVS build - they cannot be undone!
- editMenu.add(justifyLeftMenuItem);
- editMenu.add(justifyRightMenuItem);
- editMenu.addSeparator();
+ // Excluded from Jalview 2.5 release - undo needs to be implemented.
+ // editMenu.add(justifyLeftMenuItem);
+ // editMenu.add(justifyRightMenuItem);
+ // editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
viewMenu.add(newView);
viewMenu.add(expandViews);
viewMenu.add(hideMenu);
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
- viewMenu.add(annotationPanelMenuItem);
+ 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(showConsensusProfile);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
- viewMenu.add(autoAnnMenu);
+ annotationsMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(showSeqFeatures);
- //viewMenu.add(showSeqFeaturesHeight);
-
- viewMenu.add(featureSettings);
+ // viewMenu.add(showSeqFeaturesHeight);
+
+ viewMenu.add(openFeatureSettings);
tooltipSettingsMenu.add(showDbRefsMenuitem);
tooltipSettingsMenu.add(showNpFeatsMenuitem);
viewMenu.add(tooltipSettingsMenu);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
+ // colourMenu.add(covariationColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
+ calculateMenu.add(cdna);
calculateMenu.add(showProducts);
calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
calculateMenu.add(extractScores);
- webServiceNoServices = new JMenuItem("<No Services>");
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
- calculateTree.add(averageDistanceTreeMenuItem);
- calculateTree.add(neighbourTreeMenuItem);
- calculateTree.add(avDistanceTreeBlosumMenuItem);
- calculateTree.add(njTreeBlosumMenuItem);
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
+ jMenu2.add(createBioJS);
+ jMenu2.add(createSVG);
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
jMenu3.add(showAllColumns);
jMenu3.add(showAllSeqs);
+ jMenu3.add(showAllhidden);
hideMenu.add(hideSelColumns);
hideMenu.add(hideSelSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
formatMenu.add(colourTextMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelsMenuItem);
- formatMenu.add(showUnconservedMenuItem);
+ formatMenu.add(showNonconservedMenuItem);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
- selectMenu.add(deleteGroups);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
+ calculateMenu.add(expandAlignment);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ /**
+ * 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);
+ }
+
+ protected void viewAsCdna_actionPerformed()
+ {
+ }
+
+ protected void alignCdna_actionPerformed()
+ {
+ }
+
+ protected void linkCdna_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking sort annotations by type.
+ *
+ * @param sortOrder
+ */
+ protected void sortAnnotations_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking Show all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void showAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(true, forSequences, forAlignment);
+ }
+
+ /**
+ * Action on clicking Hide all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(false, forSequences, forAlignment);
+ }
+
+ /**
+ * Set the visibility of annotations to true or false. Can act on
+ * sequence-related annotations, or alignment-related, or both.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
+ {
+
+ }
+
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
}
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
- protected void showConsensusProfile_actionPerformed(ActionEvent e)
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showSeqFeaturesHeight_actionPerformed(
ActionEvent actionEvent)
{
// TODO Auto-generated method stub
-
+
}
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void followHighlight_actionPerformed()
{
// TODO Auto-generated method stub
-
+
}
protected void showNpFeats_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showDbRefs_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
- }
- protected void centreColumnLabels_actionPerformed(ActionEvent e)
- {
}
- protected void showProducts_actionPerformed(ActionEvent e)
+ protected void centreColumnLabels_actionPerformed(ActionEvent e)
{
}
{
}
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
protected void closeMenuItem_actionPerformed(boolean b)
{
}
{
}
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
{
}
+ protected void createGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void copy_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)
+ {
+
+ }
+
+ /**
+ * Template method to handle the 'Color T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+ {
+
}
protected void jpred_actionPerformed(ActionEvent e)
}
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void associatedData_actionPerformed(ActionEvent e)
{
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void showAllSeqs_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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff