+ renderGapsMenuItem_actionPerformed(e);
+ }
+ });
+
+ JMenuItem findMenuItem = new JMenuItem(
+ MessageManager.getString("action.find"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.find_tip")));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ findMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+
+ abovePIDThreshold.setText(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed(e);
+ }
+ });
+ showSeqFeatures.setText(MessageManager
+ .getString("label.show_sequence_features"));
+ showSeqFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ showSeqFeatures_actionPerformed(actionEvent);
+ }
+ });
+ /*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+ * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
+ * void actionPerformed(ActionEvent actionEvent) {
+ * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
+ */
+ showDbRefsMenuitem.setText(MessageManager
+ .getString("label.show_database_refs"));
+ showDbRefsMenuitem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showDbRefs_actionPerformed(e);
+ }
+
+ });
+ showNpFeatsMenuitem.setText(MessageManager
+ .getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showNpFeats_actionPerformed(e);
+ }
+
+ });
+ showGroupConservation.setText(MessageManager
+ .getString("label.group_conservation"));
+ showGroupConservation.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConservation_actionPerformed(e);
+ }
+
+ });
+
+ showGroupConsensus.setText(MessageManager
+ .getString("label.group_consensus"));
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConsensus_actionPerformed(e);
+ }
+
+ });
+ showConsensusHistogram.setText(MessageManager
+ .getString("label.show_consensus_histogram"));
+ showConsensusHistogram.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showConsensusHistogram_actionPerformed(e);
+ }
+
+ });
+ showSequenceLogo.setText(MessageManager
+ .getString("label.show_consensus_logo"));
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ normaliseSequenceLogo.setText(MessageManager
+ .getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ normaliseSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ applyAutoAnnotationSettings.setText(MessageManager
+ .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyAutoAnnotationSettings_actionPerformed(e);
+ }
+ });
+
+ ButtonGroup buttonGroup = new ButtonGroup();
+ final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_first"));
+ final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_last"));
+ buttonGroup.add(showAutoFirst);
+ buttonGroup.add(showAutoLast);
+ final boolean autoFirst = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+ showAutoFirst.setSelected(autoFirst);
+ setShowAutoCalculatedAbove(autoFirst);
+ showAutoFirst.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+ showAutoLast.setSelected(!showAutoFirst.isSelected());
+ showAutoLast.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ tcoffeeColorScheme_actionPerformed(e);
+ }
+ });
+
+ JMenuItem deleteGroups = new JMenuItem(
+ MessageManager.getString("action.undefine_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteGroups_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
+ JMenuItem createGroup = new JMenuItem(
+ MessageManager.getString("action.create_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroup_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
+ JMenuItem unGroup = new JMenuItem(
+ MessageManager.getString("action.remove_group"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroup_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
+ copy.setText(MessageManager.getString("action.copy"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, copy, al);
+
+ cut.setText(MessageManager.getString("action.cut"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, cut, al);
+
+ JMenuItem delete = new JMenuItem(
+ MessageManager.getString("action.delete"));
+ delete.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ delete_actionPerformed(e);
+ }
+ });
+
+ pasteMenu.setText(MessageManager.getString("action.paste"));
+ JMenuItem pasteNew = new JMenuItem(
+ MessageManager.getString("label.to_new_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteNew_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteNew, al);
+
+ JMenuItem pasteThis = new JMenuItem(
+ MessageManager.getString("label.to_this_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteThis_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
+ applyToAllGroups.setText(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyToAllGroups_actionPerformed(e);
+ }
+ });
+ JMenuItem createPNG = new JMenuItem("PNG");
+ createPNG.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createPNG(null);
+ }
+ });
+ createPNG.setActionCommand(MessageManager
+ .getString("label.save_png_image"));
+
+ JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
+ font.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ font_actionPerformed(e);
+ }
+ });
+ seqLimits.setText(MessageManager
+ .getString("label.show_sequence_limits"));
+ seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ seqLimit_actionPerformed(e);
+ }
+ });
+ JMenuItem epsFile = new JMenuItem("EPS");
+ epsFile.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createEPS(null);
+ }
+ });
+
+ JMenuItem createSVG = new JMenuItem("SVG");
+ createSVG.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSVG(null);
+ }
+ });
+
+ JMenuItem loadTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.load_associated_tree"));
+ loadTreeMenuItem.setActionCommand(MessageManager
+ .getString("label.load_tree_for_sequence_set"));
+ loadTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeMenuItem_actionPerformed(e);
+ }
+ });
+
+ scaleAbove.setVisible(false);
+ scaleAbove.setText(MessageManager.getString("action.scale_above"));
+ scaleAbove.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleAbove_actionPerformed(e);
+ }
+ });
+ scaleLeft.setVisible(false);
+ scaleLeft.setSelected(true);
+ scaleLeft.setText(MessageManager.getString("action.scale_left"));
+ scaleLeft.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleLeft_actionPerformed(e);
+ }
+ });
+ scaleRight.setVisible(false);
+ scaleRight.setSelected(true);
+ scaleRight.setText(MessageManager.getString("action.scale_right"));
+ scaleRight.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleRight_actionPerformed(e);
+ }
+ });
+ centreColumnLabelsMenuItem.setVisible(true);
+ centreColumnLabelsMenuItem.setState(false);
+ centreColumnLabelsMenuItem.setText(MessageManager
+ .getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ centreColumnLabels_actionPerformed(e);
+ }
+ });
+ followHighlightMenuItem.setVisible(true);
+ followHighlightMenuItem.setState(true);
+ followHighlightMenuItem.setText(MessageManager
+ .getString("label.automatic_scrolling"));
+ followHighlightMenuItem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ followHighlight_actionPerformed();
+ }
+
+ });
+
+ JMenuItem modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_thereshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed(e);
+ }
+ });
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_thereshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed(e);
+ }
+ });
+ sortByTreeMenu
+ .setText(MessageManager.getString("action.by_tree_order"));
+ sort.setText(MessageManager.getString("action.sort"));
+ sort.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ buildTreeMenu();
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+ sortByAnnotScore.setText(MessageManager
+ .getString("label.sort_by_score"));
+ sort.add(sortByAnnotScore);
+ sort.addMenuListener(new javax.swing.event.MenuListener()
+ {
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ });
+ sortByAnnotScore.setVisible(false);
+
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree"));
+
+ padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
+ padGapsMenuitem.setState(jalview.bin.Cache
+ .getDefault("PAD_GAPS", false));
+ padGapsMenuitem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ padGapsMenuitem_actionPerformed(e);
+ }
+ });
+ JMenuItem vamsasStore = new JMenuItem(
+ MessageManager.getString("label.vamsas_store"));
+ vamsasStore.setVisible(false);
+ vamsasStore.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStore_actionPerformed(e);
+ }
+ });
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
+ showTranslation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(e);
+ }
+ });
+ showReverse.setText(MessageManager.getString("label.reverse"));
+ showReverse.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showReverse_actionPerformed(false);
+ }
+ });
+ showReverseComplement.setText(MessageManager
+ .getString("label.reverse_complement"));
+ showReverseComplement.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showReverse_actionPerformed(true);
+ }
+ });
+
+ JMenuItem extractScores = new JMenuItem(
+ MessageManager.getString("label.extract_scores"));
+ extractScores.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ extractScores_actionPerformed(e);