+ 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();
+ }
+
+ });
+
+ sortByTreeMenu
+ .setText(MessageManager.getString("action.by_tree_order"));
+ sort.setText(MessageManager.getString("action.sort"));
+ sort.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ buildTreeSortMenu();
+ }
+
+ @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_pca"));
+
+ padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
+ padGapsMenuitem
+ .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ padGapsMenuitem_actionPerformed(e);
+ }
+ });
+ JMenuItem vamsasStore = new JMenuItem(
+ MessageManager.getString("label.vamsas_store"));
+ vamsasStore.setVisible(false);
+ vamsasStore.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStore_actionPerformed(e);
+ }
+ });
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
+ showTranslation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(e);
+ }
+ });
+ showReverse.setText(MessageManager.getString("label.reverse"));
+ showReverse.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showReverse_actionPerformed(false);
+ }
+ });
+ showReverseComplement
+ .setText(MessageManager.getString("label.reverse_complement"));
+ showReverseComplement.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showReverse_actionPerformed(true);
+ }
+ });
+
+ JMenuItem extractScores = new JMenuItem(
+ MessageManager.getString("label.extract_scores"));
+ extractScores.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ extractScores_actionPerformed(e);
+ }
+ });
+ extractScores.setVisible(true);
+ // JBPNote: TODO: make gui for regex based score extraction
+
+ // for show products actions see AlignFrame.canShowProducts
+ showProducts.setText(MessageManager.getString("label.get_cross_refs"));
+
+ runGroovy.setText(MessageManager.getString("label.run_groovy"));
+ runGroovy.setToolTipText(
+ MessageManager.getString("label.run_groovy_tip"));
+ runGroovy.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ runGroovy_actionPerformed();
+ }
+ });
+
+ JMenuItem openFeatureSettings = new JMenuItem(
+ MessageManager.getString("action.feature_settings"));
+ openFeatureSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ featureSettings_actionPerformed(e);
+ }
+ });
+ JMenuItem fetchSequence = new JMenuItem(
+ MessageManager.getString("label.fetch_sequences"));
+ fetchSequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fetchSequence_actionPerformed(e);
+ }
+ });
+
+ JMenuItem associatedData = new JMenuItem(
+ MessageManager.getString("label.load_features_annotations"));
+ associatedData.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ associatedData_actionPerformed(e);
+ }
+ });
+ loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+ loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+ loadVcf.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadVcf_actionPerformed();
+ }
+ });
+ autoCalculate.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setState(
+ jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ autoCalculate_actionPerformed(e);
+ }
+ });
+ sortByTree.setText(
+ MessageManager.getString("label.sort_alignment_new_tree"));
+ sortByTree.setToolTipText("<html>" + MessageManager.getString(
+ "label.enable_automatically_sort_alignment_when_open_new_tree"));
+ sortByTree
+ .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ sortByTree.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortByTreeOption_actionPerformed(e);
+ }
+ });
+
+ listenToViewSelections.setText(
+ MessageManager.getString("label.listen_for_selections"));
+ listenToViewSelections
+ .setToolTipText("<html>" + MessageManager.getString(
+ "label.selections_mirror_selections_made_same_sequences_other_views"));
+ listenToViewSelections.setState(false);
+ listenToViewSelections.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ listenToViewSelections_actionPerformed(e);
+ }
+ });
+
+ JMenu addSequenceMenu = new JMenu(
+ MessageManager.getString("label.add_sequences"));
+ JMenuItem addFromFile = new JMenuItem(
+ MessageManager.getString("label.from_file"));
+ addFromFile.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromFile_actionPerformed(e);
+ }
+ });
+ JMenuItem addFromText = new JMenuItem(
+ MessageManager.getString("label.from_textbox"));
+ addFromText.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromText_actionPerformed(e);
+ }
+ });
+ JMenuItem addFromURL = new JMenuItem(
+ MessageManager.getString("label.from_url"));
+ addFromURL.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromURL_actionPerformed(e);
+ }
+ });
+ JMenuItem exportFeatures = new JMenuItem(
+ MessageManager.getString("label.export_features"));
+ exportFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ exportFeatures_actionPerformed(e);
+ }
+ });
+ JMenuItem exportAnnotations = new JMenuItem(
+ MessageManager.getString("label.export_annotations"));
+ exportAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ exportAnnotations_actionPerformed(e);
+ }
+ });
+ statusPanel.setLayout(new GridLayout());
+ JMenuItem showAllSeqs = new JMenuItem(
+ MessageManager.getString("label.all_sequences"));
+ showAllSeqs.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
+ showAllSeqs.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllSeqs_actionPerformed(e);
+ }
+ });
+ JMenuItem showAllColumns = new JMenuItem(
+ MessageManager.getString("label.all_columns"));
+ showAllColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
+ showAllColumns.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllColumns_actionPerformed(e);
+ }
+ });
+ JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
+ JMenuItem hideSelSequences = new JMenuItem(
+ MessageManager.getString("label.selected_sequences"));
+ hideSelSequences.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
+ hideSelSequences.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelSequences_actionPerformed(e);
+ }
+ });
+ JMenuItem hideSelColumns = new JMenuItem(
+ MessageManager.getString("label.selected_columns"));
+ hideSelColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
+ hideSelColumns.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelColumns_actionPerformed(e);
+ }
+ });
+ JMenuItem hideAllSelection = new JMenuItem(
+ MessageManager.getString("label.selected_region"));
+ hideAllSelection.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllSelection_actionPerformed(e);
+ }
+ });
+ // TODO: should be hidden if no selection exists.
+ JMenuItem hideAllButSelection = new JMenuItem(
+ MessageManager.getString("label.all_but_selected_region"));
+ hideAllButSelection.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllButSelection_actionPerformed(e);
+ }
+ });
+ JMenuItem showAllhidden = new JMenuItem(
+ MessageManager.getString("label.all_sequences_columns"));
+ showAllhidden.setToolTipText(MessageManager
+ .getString("label.toggles_visibility_hidden_selected_regions"));
+ showAllhidden.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllhidden_actionPerformed(e);
+ }
+ });
+ hiddenMarkers.setText(
+ MessageManager.getString("action.show_hidden_markers"));
+ hiddenMarkers.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hiddenMarkers_actionPerformed(e);
+ }
+ });
+
+ JMenuItem invertColSel = new JMenuItem(
+ MessageManager.getString("action.invert_column_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK,
+ false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ invertColSel_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
+ showComplementMenuItem.setVisible(false);
+ showComplementMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showComplement_actionPerformed(showComplementMenuItem.getState());
+ }
+ });
+
+ tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ JTabbedPane pane = (JTabbedPane) evt.getSource();
+ int sel = pane.getSelectedIndex();
+ tabSelectionChanged(sel);
+ }
+ });
+ tabbedPane.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (e.isPopupTrigger()) // Mac
+ {
+ tabbedPane_mousePressed(e);
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ if (e.isPopupTrigger()) // Windows
+ {
+ tabbedPane_mousePressed(e);
+ }
+ }
+ });
+ tabbedPane.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ tabbedPane_focusGained(e);
+ }
+ });
+
+ JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ save_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, save, al);
+
+ reload.setEnabled(false);
+ reload.setText(MessageManager.getString("action.reload"));
+ reload.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ reload_actionPerformed(e);
+ }
+ });
+
+ JMenuItem newView = new JMenuItem(
+ MessageManager.getString("action.new_view"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newView_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, newView, al);
+
+ tabbedPane.setToolTipText("<html><i>"
+ + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ + "</i></html>");
+
+ formatMenu.setText(MessageManager.getString("action.format"));
+ JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
+ idRightAlign.setText(
+ MessageManager.getString("label.right_align_sequence_id"));
+ idRightAlign.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ idRightAlign_actionPerformed(e);
+ }
+ });
+
+ gatherViews.setEnabled(false);
+ gatherViews.setText(MessageManager.getString("action.gather_views"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ gatherViews_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, gatherViews, al);
+
+ expandViews.setEnabled(false);
+ expandViews.setText(MessageManager.getString("action.expand_views"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ expandViews_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
+ JMenuItem pageSetup = new JMenuItem(
+ MessageManager.getString("action.page_setup"));
+ pageSetup.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pageSetup_actionPerformed(e);
+ }
+ });
+ JMenuItem alignmentProperties = new JMenuItem(
+ MessageManager.getString("label.alignment_props"));
+ alignmentProperties.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alignmentProperties();
+ }
+ });
+ JMenuItem selectHighlighted = new JMenuItem(
+ MessageManager.getString("action.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.select_highlighted_columns"));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectHighlightedColumns_actionPerformed(actionEvent);
+ }
+ };
+ selectHighlighted.addActionListener(al);
+ JMenu tooltipSettingsMenu = new JMenu(
+ MessageManager.getString("label.sequence_id_tooltip"));
+ JMenu autoAnnMenu = new JMenu(
+ MessageManager.getString("label.autocalculated_annotation"));
+
+ JMenu exportImageMenu = new JMenu(
+ MessageManager.getString("label.export_image"));
+ JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
+ alignFrameMenuBar.add(fileMenu);
+ alignFrameMenuBar.add(editMenu);
+ alignFrameMenuBar.add(selectMenu);
+ alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(annotationsMenu);
+ alignFrameMenuBar.add(formatMenu);
+ alignFrameMenuBar.add(colourMenu);
+ alignFrameMenuBar.add(calculateMenu);
+ alignFrameMenuBar.add(webService);
+
+ fileMenu.add(fetchSequence);
+ fileMenu.add(addSequenceMenu);
+ fileMenu.add(reload);
+ fileMenu.addSeparator();
+ fileMenu.add(vamsasStore);
+ fileMenu.add(save);
+ fileMenu.add(saveAs);
+ fileMenu.add(outputTextboxMenu);
+ fileMenu.add(pageSetup);
+ fileMenu.add(printMenuItem);
+ fileMenu.addSeparator();
+ fileMenu.add(exportImageMenu);
+ fileMenu.add(exportFeatures);
+ fileMenu.add(exportAnnotations);
+ fileMenu.add(loadTreeMenuItem);
+ fileMenu.add(associatedData);
+ fileMenu.add(loadVcf);
+ fileMenu.addSeparator();
+ fileMenu.add(closeMenuItem);
+
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
+ editMenu.add(undoMenuItem);
+ editMenu.add(redoMenuItem);
+ editMenu.add(cut);
+ editMenu.add(copy);
+ editMenu.add(pasteMenu);
+ editMenu.add(delete);
+ editMenu.addSeparator();
+ editMenu.add(remove2LeftMenuItem);
+ editMenu.add(remove2RightMenuItem);
+ editMenu.add(removeGappedColumnMenuItem);
+ editMenu.add(removeAllGapsMenuItem);
+ editMenu.add(removeRedundancyMenuItem);
+ editMenu.addSeparator();
+ // dont add these yet in the CVS build - they cannot be undone!
+ // Excluded from Jalview 2.5 release - undo needs to be implemented.
+ // editMenu.add(justifyLeftMenuItem);
+ // editMenu.add(justifyRightMenuItem);
+ // editMenu.addSeparator();
+ editMenu.add(padGapsMenuitem);
+
+ showMenu.add(showAllColumns);
+ showMenu.add(showAllSeqs);
+ showMenu.add(showAllhidden);
+ hideMenu.add(hideSelColumns);
+ hideMenu.add(hideSelSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+ viewMenu.add(newView);
+ viewMenu.add(expandViews);
+ viewMenu.add(gatherViews);
+ viewMenu.addSeparator();
+ viewMenu.add(showMenu);
+ viewMenu.add(hideMenu);
+ viewMenu.add(showComplementMenuItem);
+ viewMenu.addSeparator();
+ viewMenu.add(followHighlightMenuItem);
+ viewMenu.addSeparator();
+ viewMenu.add(showSeqFeatures);
+ // viewMenu.add(showSeqFeaturesHeight);
+ viewMenu.add(openFeatureSettings);
+ tooltipSettingsMenu.add(showDbRefsMenuitem);
+ tooltipSettingsMenu.add(showNpFeatsMenuitem);
+ viewMenu.add(tooltipSettingsMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(alignmentProperties);
+ viewMenu.addSeparator();
+ viewMenu.add(overviewMenuItem);
+
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllAlAnnotations);
+ annotationsMenu.add(hideAllAlAnnotations);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllSeqAnnotations);
+ annotationsMenu.add(hideAllSeqAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ annotationsMenu.add(autoAnnMenu);
+
+ sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
+ calculateMenu.add(sort);
+ calculateMenu.add(calculateTree);
+ calculateMenu.addSeparator();
+ calculateMenu.add(pairwiseAlignmentMenuItem);
+ calculateMenu.addSeparator();
+ calculateMenu.add(showTranslation);
+ calculateMenu.add(showReverse);
+ calculateMenu.add(showReverseComplement);
+ calculateMenu.add(showProducts);
+ calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
+ calculateMenu.addSeparator();
+ calculateMenu.add(expandAlignment);
+ calculateMenu.add(extractScores);
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
+ webService.add(webServiceNoServices);
+ exportImageMenu.add(htmlMenuItem);
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ exportImageMenu.add(createBioJS);
+ exportImageMenu.add(createSVG);
+ addSequenceMenu.add(addFromFile);
+ addSequenceMenu.add(addFromText);
+ addSequenceMenu.add(addFromURL);
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+
+ formatMenu.add(font);
+ formatMenu.addSeparator();
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(seqLimits);
+ formatMenu.add(idRightAlign);
+ formatMenu.add(hiddenMarkers);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelsMenuItem);
+ formatMenu.add(showNonconservedMenuItem);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
+ selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
+ selectMenu.add(selectHighlighted);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ protected void loadVcf_actionPerformed()
+ {
+ }
+
+ /**
+ * Constructs the entries on the Colour menu (but does not add them to the
+ * menu).
+ */
+ protected void initColourMenu()
+ {
+ applyToAllGroups = new JCheckBoxMenuItem(
+ MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
+ }
+ });
+
+ textColour = new JMenuItem(
+ MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+
+ conservationMenuItem = new JCheckBoxMenuItem(
+ MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
+ }
+ });
+
+ abovePIDThreshold = new JCheckBoxMenuItem(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
+ }
+ });
+ modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+ modifyConservation = new JMenuItem(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();