2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.analysis.GeneticCodeI;
25 import jalview.analysis.GeneticCodes;
26 import jalview.api.SplitContainerI;
27 import jalview.bin.Cache;
28 import jalview.gui.JvSwingUtils;
29 import jalview.gui.Preferences;
30 import jalview.io.FileFormats;
31 import jalview.schemes.ResidueColourScheme;
32 import jalview.util.MessageManager;
33 import jalview.util.Platform;
35 import java.awt.BorderLayout;
36 import java.awt.Color;
37 import java.awt.GridLayout;
38 import java.awt.Toolkit;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.awt.event.FocusAdapter;
42 import java.awt.event.FocusEvent;
43 import java.awt.event.KeyEvent;
44 import java.awt.event.MouseAdapter;
45 import java.awt.event.MouseEvent;
46 import java.util.HashMap;
49 import javax.swing.BorderFactory;
50 import javax.swing.ButtonGroup;
51 import javax.swing.JCheckBoxMenuItem;
52 import javax.swing.JInternalFrame;
53 import javax.swing.JLabel;
54 import javax.swing.JMenu;
55 import javax.swing.JMenuBar;
56 import javax.swing.JMenuItem;
57 import javax.swing.JPanel;
58 import javax.swing.JRadioButtonMenuItem;
59 import javax.swing.JTabbedPane;
60 import javax.swing.KeyStroke;
61 import javax.swing.event.ChangeEvent;
62 import javax.swing.event.MenuEvent;
63 import javax.swing.event.MenuListener;
65 public class GAlignFrame extends JInternalFrame
67 protected JMenuBar alignFrameMenuBar = new JMenuBar();
69 protected JMenuItem closeMenuItem = new JMenuItem();
71 protected JMenu webService = new JMenu();
73 protected JMenuItem webServiceNoServices;
75 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
77 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
79 protected JMenu sortByAnnotScore = new JMenu();
81 protected JLabel statusBar = new JLabel();
83 protected JMenu outputTextboxMenu = new JMenu();
85 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
87 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
89 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
91 protected JMenuItem undoMenuItem = new JMenuItem();
93 protected JMenuItem redoMenuItem = new JMenuItem();
95 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
97 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
99 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
101 JMenuItem copy = new JMenuItem();
103 JMenuItem cut = new JMenuItem();
105 JMenu pasteMenu = new JMenu();
107 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
109 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
111 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
113 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
115 protected JCheckBoxMenuItem applyToAllGroups;
117 protected JMenu colourMenu = new JMenu();
119 protected JMenuItem textColour;
121 protected JCheckBoxMenuItem conservationMenuItem;
123 protected JMenuItem modifyConservation;
125 protected JCheckBoxMenuItem abovePIDThreshold;
127 protected JMenuItem modifyPID;
129 protected JRadioButtonMenuItem annotationColour;
131 protected JMenu sortByTreeMenu = new JMenu();
133 protected JMenu sort = new JMenu();
135 protected JMenuItem calculateTree = new JMenuItem();
137 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
139 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
141 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
143 protected JMenu showTranslation = new JMenu();
145 protected JMenuItem showReverse = new JMenuItem();
147 protected JMenuItem showReverseComplement = new JMenuItem();
149 protected JMenu showProducts = new JMenu();
151 protected JMenuItem runGroovy = new JMenuItem();
153 protected JMenuItem loadVcf;
155 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
157 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
159 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
161 protected JPanel statusPanel = new JPanel();
163 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
165 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
167 protected JMenuItem showAllAlAnnotations = new JMenuItem();
169 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
171 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
173 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
175 protected JTabbedPane tabbedPane = new JTabbedPane();
177 protected JMenuItem reload = new JMenuItem();
179 protected JMenu formatMenu = new JMenu();
181 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
183 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
185 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
187 protected JMenuItem gatherViews = new JMenuItem();
189 protected JMenuItem expandViews = new JMenuItem();
191 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
193 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
203 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
205 private SplitContainerI splitFrame;
207 protected JCheckBoxMenuItem sortAnnBySequence;
209 protected JCheckBoxMenuItem sortAnnByLabel;
211 protected JMenu annotationsMenu;
218 setJMenuBar(alignFrameMenuBar);
220 // dynamically fill save as menu with available formats
221 for (String ff : FileFormats.getInstance().getWritableFormats(true))
223 JMenuItem item = new JMenuItem(ff);
225 item.addActionListener(new ActionListener()
228 public void actionPerformed(ActionEvent e)
230 outputText_actionPerformed(e);
234 outputTextboxMenu.add(item);
236 } catch (Exception e)
238 System.err.println(e.toString());
241 if (!Platform.isAMac())
243 closeMenuItem.setMnemonic('C');
244 outputTextboxMenu.setMnemonic('T');
245 undoMenuItem.setMnemonic('Z');
246 redoMenuItem.setMnemonic('0');
247 copy.setMnemonic('C');
248 cut.setMnemonic('U');
249 pasteMenu.setMnemonic('P');
250 reload.setMnemonic('R');
254 private void jbInit() throws Exception
258 JMenuItem saveAs = new JMenuItem(
259 MessageManager.getString("action.save_as"));
260 ActionListener al = new ActionListener()
263 public void actionPerformed(ActionEvent e)
265 saveAs_actionPerformed(e);
269 // FIXME getDefaultToolkit throws an exception in Headless mode
270 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
271 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
272 | KeyEvent.SHIFT_MASK,
274 addMenuActionAndAccelerator(keyStroke, saveAs, al);
276 closeMenuItem.setText(MessageManager.getString("action.close"));
277 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
278 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
279 al = new ActionListener()
282 public void actionPerformed(ActionEvent e)
284 closeMenuItem_actionPerformed(false);
287 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
289 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
290 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
291 annotationsMenu = new JMenu(
292 MessageManager.getString("action.annotations"));
293 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
294 colourMenu.setText(MessageManager.getString("action.colour"));
295 JMenu calculateMenu = new JMenu(
296 MessageManager.getString("action.calculate"));
297 webService.setText(MessageManager.getString("action.web_service"));
298 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
299 MessageManager.getString("action.select_all"));
300 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
301 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
302 al = new ActionListener()
305 public void actionPerformed(ActionEvent e)
307 selectAllSequenceMenuItem_actionPerformed(e);
310 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
312 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
313 MessageManager.getString("action.deselect_all"));
314 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
315 al = new ActionListener()
318 public void actionPerformed(ActionEvent e)
320 deselectAllSequenceMenuItem_actionPerformed(e);
323 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
325 JMenuItem invertSequenceMenuItem = new JMenuItem(
326 MessageManager.getString("action.invert_sequence_selection"));
327 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
328 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
329 al = new ActionListener()
332 public void actionPerformed(ActionEvent e)
334 invertSequenceMenuItem_actionPerformed(e);
337 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
339 JMenuItem grpsFromSelection = new JMenuItem(
340 MessageManager.getString("action.make_groups_selection"));
341 grpsFromSelection.addActionListener(new ActionListener()
344 public void actionPerformed(ActionEvent e)
346 makeGrpsFromSelection_actionPerformed(e);
349 JMenuItem expandAlignment = new JMenuItem(
350 MessageManager.getString("action.view_flanking_regions"));
351 expandAlignment.setToolTipText(
352 MessageManager.getString("label.view_flanking_regions"));
353 expandAlignment.addActionListener(new ActionListener()
356 public void actionPerformed(ActionEvent e)
361 JMenuItem remove2LeftMenuItem = new JMenuItem(
362 MessageManager.getString("action.remove_left"));
363 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
364 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
365 al = new ActionListener()
368 public void actionPerformed(ActionEvent e)
370 remove2LeftMenuItem_actionPerformed(e);
373 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
375 JMenuItem remove2RightMenuItem = new JMenuItem(
376 MessageManager.getString("action.remove_right"));
377 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
378 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
379 al = new ActionListener()
382 public void actionPerformed(ActionEvent e)
384 remove2RightMenuItem_actionPerformed(e);
387 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
389 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
390 MessageManager.getString("action.remove_empty_columns"));
391 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
392 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
393 al = new ActionListener()
396 public void actionPerformed(ActionEvent e)
398 removeGappedColumnMenuItem_actionPerformed(e);
401 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
403 JMenuItem removeAllGapsMenuItem = new JMenuItem(
404 MessageManager.getString("action.remove_all_gaps"));
405 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
406 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
407 | KeyEvent.SHIFT_MASK,
409 al = new ActionListener()
412 public void actionPerformed(ActionEvent e)
414 removeAllGapsMenuItem_actionPerformed(e);
417 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
419 JMenuItem justifyLeftMenuItem = new JMenuItem(
420 MessageManager.getString("action.left_justify_alignment"));
421 justifyLeftMenuItem.addActionListener(new ActionListener()
424 public void actionPerformed(ActionEvent e)
426 justifyLeftMenuItem_actionPerformed(e);
429 JMenuItem justifyRightMenuItem = new JMenuItem(
430 MessageManager.getString("action.right_justify_alignment"));
431 justifyRightMenuItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent e)
436 justifyRightMenuItem_actionPerformed(e);
439 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
440 viewBoxesMenuItem.setState(true);
441 viewBoxesMenuItem.addActionListener(new ActionListener()
444 public void actionPerformed(ActionEvent e)
446 viewBoxesMenuItem_actionPerformed(e);
449 viewTextMenuItem.setText(MessageManager.getString("action.text"));
450 viewTextMenuItem.setState(true);
451 viewTextMenuItem.addActionListener(new ActionListener()
454 public void actionPerformed(ActionEvent e)
456 viewTextMenuItem_actionPerformed(e);
459 showNonconservedMenuItem
460 .setText(MessageManager.getString("label.show_non_conserved"));
461 showNonconservedMenuItem.setState(false);
462 showNonconservedMenuItem.addActionListener(new ActionListener()
465 public void actionPerformed(ActionEvent e)
467 showUnconservedMenuItem_actionPerformed(e);
470 JMenuItem sortPairwiseMenuItem = new JMenuItem(
471 MessageManager.getString("action.by_pairwise_id"));
472 sortPairwiseMenuItem.addActionListener(new ActionListener()
475 public void actionPerformed(ActionEvent e)
477 sortPairwiseMenuItem_actionPerformed(e);
480 JMenuItem sortIDMenuItem = new JMenuItem(
481 MessageManager.getString("action.by_id"));
482 sortIDMenuItem.addActionListener(new ActionListener()
485 public void actionPerformed(ActionEvent e)
487 sortIDMenuItem_actionPerformed(e);
490 JMenuItem sortLengthMenuItem = new JMenuItem(
491 MessageManager.getString("action.by_length"));
492 sortLengthMenuItem.addActionListener(new ActionListener()
495 public void actionPerformed(ActionEvent e)
497 sortLengthMenuItem_actionPerformed(e);
500 JMenuItem sortGroupMenuItem = new JMenuItem(
501 MessageManager.getString("action.by_group"));
502 sortGroupMenuItem.addActionListener(new ActionListener()
505 public void actionPerformed(ActionEvent e)
507 sortGroupMenuItem_actionPerformed(e);
511 JMenuItem removeRedundancyMenuItem = new JMenuItem(
512 MessageManager.getString("action.remove_redundancy"));
513 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
514 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
515 al = new ActionListener()
518 public void actionPerformed(ActionEvent e)
520 removeRedundancyMenuItem_actionPerformed(e);
523 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
525 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
526 MessageManager.getString("action.pairwise_alignment"));
527 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
530 public void actionPerformed(ActionEvent e)
532 pairwiseAlignmentMenuItem_actionPerformed(e);
536 this.getContentPane().setLayout(new BorderLayout());
537 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
538 statusBar.setBackground(Color.white);
539 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
540 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
541 statusBar.setText(MessageManager.getString("label.status_bar"));
543 .setText(MessageManager.getString("label.out_to_textbox"));
545 annotationPanelMenuItem.setActionCommand("");
546 annotationPanelMenuItem
547 .setText(MessageManager.getString("label.show_annotations"));
548 annotationPanelMenuItem
549 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
550 annotationPanelMenuItem.addActionListener(new ActionListener()
553 public void actionPerformed(ActionEvent e)
555 annotationPanelMenuItem_actionPerformed(e);
558 showAllAlAnnotations.setText(
559 MessageManager.getString("label.show_all_al_annotations"));
560 final boolean isAnnotationPanelShown = annotationPanelMenuItem
562 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
563 showAllAlAnnotations.addActionListener(new ActionListener()
566 public void actionPerformed(ActionEvent e)
568 showAllAnnotations_actionPerformed(false, true);
571 hideAllAlAnnotations.setText(
572 MessageManager.getString("label.hide_all_al_annotations"));
573 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
574 hideAllAlAnnotations.addActionListener(new ActionListener()
577 public void actionPerformed(ActionEvent e)
579 hideAllAnnotations_actionPerformed(false, true);
582 showAllSeqAnnotations.setText(
583 MessageManager.getString("label.show_all_seq_annotations"));
584 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
585 showAllSeqAnnotations.addActionListener(new ActionListener()
588 public void actionPerformed(ActionEvent e)
590 showAllAnnotations_actionPerformed(true, false);
593 hideAllSeqAnnotations.setText(
594 MessageManager.getString("label.hide_all_seq_annotations"));
595 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
596 hideAllSeqAnnotations.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent e)
601 hideAllAnnotations_actionPerformed(true, false);
604 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
605 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
606 SequenceAnnotationOrder.NONE.name()));
607 sortAnnBySequence = new JCheckBoxMenuItem(
608 MessageManager.getString("label.sort_annotations_by_sequence"));
609 sortAnnByLabel = new JCheckBoxMenuItem(
610 MessageManager.getString("label.sort_annotations_by_label"));
612 sortAnnBySequence.setSelected(
613 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
614 sortAnnBySequence.addActionListener(new ActionListener()
617 public void actionPerformed(ActionEvent e)
619 boolean newState = sortAnnBySequence.getState();
620 sortAnnByLabel.setSelected(false);
621 setAnnotationSortOrder(
622 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
623 : SequenceAnnotationOrder.NONE);
627 sortAnnByLabel.setSelected(
628 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
629 sortAnnByLabel.addActionListener(new ActionListener()
632 public void actionPerformed(ActionEvent e)
634 boolean newState = sortAnnByLabel.getState();
635 sortAnnBySequence.setSelected(false);
636 setAnnotationSortOrder(
637 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
638 : SequenceAnnotationOrder.NONE);
642 colourTextMenuItem = new JCheckBoxMenuItem(
643 MessageManager.getString("label.colour_text"));
644 colourTextMenuItem.addActionListener(new ActionListener()
647 public void actionPerformed(ActionEvent e)
649 colourTextMenuItem_actionPerformed(e);
653 JMenuItem htmlMenuItem = new JMenuItem(
654 MessageManager.getString("label.html"));
655 htmlMenuItem.addActionListener(new ActionListener()
658 public void actionPerformed(ActionEvent e)
660 htmlMenuItem_actionPerformed(e);
664 JMenuItem createBioJS = new JMenuItem(
665 MessageManager.getString("label.biojs_html_export"));
666 createBioJS.addActionListener(new java.awt.event.ActionListener()
669 public void actionPerformed(ActionEvent e)
671 bioJSMenuItem_actionPerformed(e);
675 JMenuItem overviewMenuItem = new JMenuItem(
676 MessageManager.getString("label.overview_window"));
677 overviewMenuItem.addActionListener(new ActionListener()
680 public void actionPerformed(ActionEvent e)
682 overviewMenuItem_actionPerformed(e);
686 undoMenuItem.setEnabled(false);
687 undoMenuItem.setText(MessageManager.getString("action.undo"));
688 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
689 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
690 al = new ActionListener()
693 public void actionPerformed(ActionEvent e)
695 undoMenuItem_actionPerformed(e);
698 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
700 redoMenuItem.setEnabled(false);
701 redoMenuItem.setText(MessageManager.getString("action.redo"));
702 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
703 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
704 al = new ActionListener()
707 public void actionPerformed(ActionEvent e)
709 redoMenuItem_actionPerformed(e);
712 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
714 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
715 wrapMenuItem.addActionListener(new ActionListener()
718 public void actionPerformed(ActionEvent e)
720 wrapMenuItem_actionPerformed(e);
724 JMenuItem printMenuItem = new JMenuItem(
725 MessageManager.getString("action.print"));
726 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
727 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
728 al = new ActionListener()
731 public void actionPerformed(ActionEvent e)
733 printMenuItem_actionPerformed(e);
736 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
739 .setText(MessageManager.getString("action.show_gaps"));
740 renderGapsMenuItem.setState(true);
741 renderGapsMenuItem.addActionListener(new ActionListener()
744 public void actionPerformed(ActionEvent e)
746 renderGapsMenuItem_actionPerformed(e);
750 JMenuItem findMenuItem = new JMenuItem(
751 MessageManager.getString("action.find"));
752 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
753 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
754 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
755 MessageManager.getString("label.find_tip")));
756 al = new ActionListener()
759 public void actionPerformed(ActionEvent e)
761 findMenuItem_actionPerformed(e);
764 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
766 showSeqFeatures.setText(
767 MessageManager.getString("label.show_sequence_features"));
768 showSeqFeatures.addActionListener(new ActionListener()
771 public void actionPerformed(ActionEvent actionEvent)
773 showSeqFeatures_actionPerformed(actionEvent);
777 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
778 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
779 * void actionPerformed(ActionEvent actionEvent) {
780 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
783 .setText(MessageManager.getString("label.show_database_refs"));
784 showDbRefsMenuitem.addActionListener(new ActionListener()
788 public void actionPerformed(ActionEvent e)
790 showDbRefs_actionPerformed(e);
794 showNpFeatsMenuitem.setText(
795 MessageManager.getString("label.show_non_positional_features"));
796 showNpFeatsMenuitem.addActionListener(new ActionListener()
800 public void actionPerformed(ActionEvent e)
802 showNpFeats_actionPerformed(e);
806 showGroupConservation
807 .setText(MessageManager.getString("label.group_conservation"));
808 showGroupConservation.addActionListener(new ActionListener()
812 public void actionPerformed(ActionEvent e)
814 showGroupConservation_actionPerformed(e);
820 .setText(MessageManager.getString("label.group_consensus"));
821 showGroupConsensus.addActionListener(new ActionListener()
825 public void actionPerformed(ActionEvent e)
827 showGroupConsensus_actionPerformed(e);
831 showConsensusHistogram.setText(
832 MessageManager.getString("label.show_consensus_histogram"));
833 showConsensusHistogram.addActionListener(new ActionListener()
837 public void actionPerformed(ActionEvent e)
839 showConsensusHistogram_actionPerformed(e);
844 .setText(MessageManager.getString("label.show_consensus_logo"));
845 showSequenceLogo.addActionListener(new ActionListener()
849 public void actionPerformed(ActionEvent e)
851 showSequenceLogo_actionPerformed(e);
855 normaliseSequenceLogo
856 .setText(MessageManager.getString("label.norm_consensus_logo"));
857 normaliseSequenceLogo.addActionListener(new ActionListener()
861 public void actionPerformed(ActionEvent e)
863 normaliseSequenceLogo_actionPerformed(e);
867 applyAutoAnnotationSettings
868 .setText(MessageManager.getString("label.apply_all_groups"));
869 applyAutoAnnotationSettings.setState(false);
870 applyAutoAnnotationSettings.setVisible(true);
871 applyAutoAnnotationSettings.addActionListener(new ActionListener()
874 public void actionPerformed(ActionEvent e)
876 applyAutoAnnotationSettings_actionPerformed(e);
880 ButtonGroup buttonGroup = new ButtonGroup();
881 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
882 MessageManager.getString("label.show_first"));
883 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
884 MessageManager.getString("label.show_last"));
885 buttonGroup.add(showAutoFirst);
886 buttonGroup.add(showAutoLast);
887 final boolean autoFirst = Cache
888 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
889 showAutoFirst.setSelected(autoFirst);
890 showAutoFirst.addActionListener(new ActionListener()
893 public void actionPerformed(ActionEvent e)
895 if (setShowAutoCalculatedAbove(showAutoFirst.isSelected()))
901 showAutoLast.setSelected(!showAutoFirst.isSelected());
902 showAutoLast.addActionListener(new ActionListener()
905 public void actionPerformed(ActionEvent e)
907 if (setShowAutoCalculatedAbove(!showAutoLast.isSelected()))
914 JMenuItem deleteGroups = new JMenuItem(
915 MessageManager.getString("action.undefine_groups"));
916 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
917 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
918 al = new ActionListener()
921 public void actionPerformed(ActionEvent e)
923 deleteGroups_actionPerformed(e);
926 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
928 JMenuItem annotationColumn = new JMenuItem(
929 MessageManager.getString("action.select_by_annotation"));
930 annotationColumn.addActionListener(new ActionListener()
933 public void actionPerformed(ActionEvent e)
935 annotationColumn_actionPerformed(e);
939 JMenuItem createGroup = new JMenuItem(
940 MessageManager.getString("action.create_group"));
941 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
942 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
943 al = new ActionListener()
946 public void actionPerformed(ActionEvent e)
948 createGroup_actionPerformed(e);
951 addMenuActionAndAccelerator(keyStroke, createGroup, al);
953 JMenuItem unGroup = new JMenuItem(
954 MessageManager.getString("action.remove_group"));
955 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
956 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
957 | KeyEvent.SHIFT_MASK,
959 al = new ActionListener()
962 public void actionPerformed(ActionEvent e)
964 unGroup_actionPerformed(e);
967 addMenuActionAndAccelerator(keyStroke, unGroup, al);
969 copy.setText(MessageManager.getString("action.copy"));
970 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
971 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
973 al = new ActionListener()
976 public void actionPerformed(ActionEvent e)
978 copy_actionPerformed(e);
981 addMenuActionAndAccelerator(keyStroke, copy, al);
983 cut.setText(MessageManager.getString("action.cut"));
984 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
985 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
986 al = new ActionListener()
989 public void actionPerformed(ActionEvent e)
991 cut_actionPerformed(e);
994 addMenuActionAndAccelerator(keyStroke, cut, al);
996 JMenuItem delete = new JMenuItem(
997 MessageManager.getString("action.delete"));
998 delete.addActionListener(new ActionListener()
1001 public void actionPerformed(ActionEvent e)
1003 delete_actionPerformed(e);
1007 pasteMenu.setText(MessageManager.getString("action.paste"));
1008 JMenuItem pasteNew = new JMenuItem(
1009 MessageManager.getString("label.to_new_alignment"));
1010 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1011 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1012 | KeyEvent.SHIFT_MASK,
1014 al = new ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 pasteNew_actionPerformed(e);
1022 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1024 JMenuItem pasteThis = new JMenuItem(
1025 MessageManager.getString("label.to_this_alignment"));
1026 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1027 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1028 al = new ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 pasteThis_actionPerformed(e);
1036 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1038 JMenuItem createPNG = new JMenuItem("PNG");
1039 createPNG.addActionListener(new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1047 createPNG.setActionCommand(
1048 MessageManager.getString("label.save_png_image"));
1050 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1051 font.addActionListener(new ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 font_actionPerformed(e);
1060 MessageManager.getString("label.show_sequence_limits"));
1061 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1062 seqLimits.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 seqLimit_actionPerformed(e);
1070 JMenuItem epsFile = new JMenuItem("EPS");
1071 epsFile.addActionListener(new ActionListener()
1074 public void actionPerformed(ActionEvent e)
1080 JMenuItem createSVG = new JMenuItem("SVG");
1081 createSVG.addActionListener(new ActionListener()
1084 public void actionPerformed(ActionEvent e)
1090 JMenuItem loadTreeMenuItem = new JMenuItem(
1091 MessageManager.getString("label.load_associated_tree"));
1092 loadTreeMenuItem.setActionCommand(
1093 MessageManager.getString("label.load_tree_for_sequence_set"));
1094 loadTreeMenuItem.addActionListener(new ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 loadTreeMenuItem_actionPerformed(e);
1103 scaleAbove.setVisible(false);
1104 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1105 scaleAbove.addActionListener(new ActionListener()
1108 public void actionPerformed(ActionEvent e)
1110 scaleAbove_actionPerformed(e);
1113 scaleLeft.setVisible(false);
1114 scaleLeft.setSelected(true);
1115 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1116 scaleLeft.addActionListener(new ActionListener()
1119 public void actionPerformed(ActionEvent e)
1121 scaleLeft_actionPerformed(e);
1124 scaleRight.setVisible(false);
1125 scaleRight.setSelected(true);
1126 scaleRight.setText(MessageManager.getString("action.scale_right"));
1127 scaleRight.addActionListener(new ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 scaleRight_actionPerformed(e);
1135 centreColumnLabelsMenuItem.setVisible(true);
1136 centreColumnLabelsMenuItem.setState(false);
1137 centreColumnLabelsMenuItem.setText(
1138 MessageManager.getString("label.centre_column_labels"));
1139 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1142 public void actionPerformed(ActionEvent e)
1144 centreColumnLabels_actionPerformed(e);
1147 followHighlightMenuItem.setVisible(true);
1148 followHighlightMenuItem.setState(true);
1149 followHighlightMenuItem
1150 .setText(MessageManager.getString("label.automatic_scrolling"));
1151 followHighlightMenuItem.addActionListener(new ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 followHighlight_actionPerformed();
1163 .setText(MessageManager.getString("action.by_tree_order"));
1164 sort.setText(MessageManager.getString("action.sort"));
1165 sort.addMenuListener(new MenuListener()
1168 public void menuSelected(MenuEvent e)
1170 buildTreeSortMenu();
1174 public void menuDeselected(MenuEvent e)
1179 public void menuCanceled(MenuEvent e)
1184 .setText(MessageManager.getString("label.sort_by_score"));
1185 sort.add(sortByAnnotScore);
1186 sort.addMenuListener(new javax.swing.event.MenuListener()
1190 public void menuCanceled(MenuEvent e)
1195 public void menuDeselected(MenuEvent e)
1200 public void menuSelected(MenuEvent e)
1202 buildSortByAnnotationScoresMenu();
1205 sortByAnnotScore.setVisible(false);
1208 .setText(MessageManager.getString("action.calculate_tree_pca"));
1210 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1212 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1213 padGapsMenuitem.addActionListener(new ActionListener()
1216 public void actionPerformed(ActionEvent e)
1218 padGapsMenuitem_actionPerformed(e);
1221 JMenuItem vamsasStore = new JMenuItem(
1222 MessageManager.getString("label.vamsas_store"));
1223 vamsasStore.setVisible(false);
1224 vamsasStore.addActionListener(new ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 vamsasStore_actionPerformed(e);
1234 * Translate as cDNA with sub-menu of translation tables
1236 showTranslation.setText(MessageManager
1237 .getString("label.translate_cDNA"));
1238 boolean first = true;
1239 for (final GeneticCodeI table : GeneticCodes.getInstance()
1242 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1243 showTranslation.add(item);
1244 item.addActionListener(new ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 showTranslation_actionPerformed(table);
1254 showTranslation.addSeparator();
1259 showReverse.setText(MessageManager.getString("label.reverse"));
1260 showReverse.addActionListener(new ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 showReverse_actionPerformed(false);
1268 showReverseComplement
1269 .setText(MessageManager.getString("label.reverse_complement"));
1270 showReverseComplement.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 showReverse_actionPerformed(true);
1279 JMenuItem extractScores = new JMenuItem(
1280 MessageManager.getString("label.extract_scores"));
1281 extractScores.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent e)
1286 extractScores_actionPerformed(e);
1289 extractScores.setVisible(true);
1290 // JBPNote: TODO: make gui for regex based score extraction
1292 // for show products actions see AlignFrame.canShowProducts
1293 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1295 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1296 runGroovy.setToolTipText(
1297 MessageManager.getString("label.run_groovy_tip"));
1298 runGroovy.addActionListener(new ActionListener()
1301 public void actionPerformed(ActionEvent e)
1303 runGroovy_actionPerformed();
1307 JMenuItem openFeatureSettings = new JMenuItem(
1308 MessageManager.getString("action.feature_settings"));
1309 openFeatureSettings.addActionListener(new ActionListener()
1312 public void actionPerformed(ActionEvent e)
1314 featureSettings_actionPerformed(e);
1317 JMenuItem fetchSequence = new JMenuItem(
1318 MessageManager.getString("label.fetch_sequences"));
1319 fetchSequence.addActionListener(new ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 fetchSequence_actionPerformed(e);
1328 JMenuItem associatedData = new JMenuItem(
1329 MessageManager.getString("label.load_features_annotations"));
1330 associatedData.addActionListener(new ActionListener()
1333 public void actionPerformed(ActionEvent e)
1335 associatedData_actionPerformed(e);
1338 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1339 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1340 loadVcf.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 loadVcf_actionPerformed();
1348 autoCalculate.setText(
1349 MessageManager.getString("label.autocalculate_consensus"));
1350 autoCalculate.setState(
1351 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1352 autoCalculate.addActionListener(new ActionListener()
1355 public void actionPerformed(ActionEvent e)
1357 autoCalculate_actionPerformed(e);
1361 MessageManager.getString("label.sort_alignment_new_tree"));
1362 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1363 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1365 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1366 sortByTree.addActionListener(new ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 sortByTreeOption_actionPerformed(e);
1375 listenToViewSelections.setText(
1376 MessageManager.getString("label.listen_for_selections"));
1377 listenToViewSelections
1378 .setToolTipText("<html>" + MessageManager.getString(
1379 "label.selections_mirror_selections_made_same_sequences_other_views"));
1380 listenToViewSelections.setState(false);
1381 listenToViewSelections.addActionListener(new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 listenToViewSelections_actionPerformed(e);
1390 JMenu addSequenceMenu = new JMenu(
1391 MessageManager.getString("label.add_sequences"));
1392 JMenuItem addFromFile = new JMenuItem(
1393 MessageManager.getString("label.from_file"));
1394 addFromFile.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 addFromFile_actionPerformed(e);
1402 JMenuItem addFromText = new JMenuItem(
1403 MessageManager.getString("label.from_textbox"));
1404 addFromText.addActionListener(new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 addFromText_actionPerformed(e);
1412 JMenuItem addFromURL = new JMenuItem(
1413 MessageManager.getString("label.from_url"));
1414 addFromURL.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent e)
1419 addFromURL_actionPerformed(e);
1422 JMenuItem exportFeatures = new JMenuItem(
1423 MessageManager.getString("label.export_features"));
1424 exportFeatures.addActionListener(new ActionListener()
1427 public void actionPerformed(ActionEvent e)
1429 exportFeatures_actionPerformed(e);
1432 JMenuItem exportAnnotations = new JMenuItem(
1433 MessageManager.getString("label.export_annotations"));
1434 exportAnnotations.addActionListener(new ActionListener()
1437 public void actionPerformed(ActionEvent e)
1439 exportAnnotations_actionPerformed(e);
1442 statusPanel.setLayout(new GridLayout());
1443 JMenuItem showAllSeqs = new JMenuItem(
1444 MessageManager.getString("label.all_sequences"));
1445 showAllSeqs.setToolTipText(
1446 MessageManager.getString("label.toggle_sequence_visibility"));
1447 showAllSeqs.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 showAllSeqs_actionPerformed(e);
1455 JMenuItem showAllColumns = new JMenuItem(
1456 MessageManager.getString("label.all_columns"));
1457 showAllColumns.setToolTipText(
1458 MessageManager.getString("label.toggle_columns_visibility"));
1459 showAllColumns.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 showAllColumns_actionPerformed(e);
1467 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1468 JMenuItem hideSelSequences = new JMenuItem(
1469 MessageManager.getString("label.selected_sequences"));
1470 hideSelSequences.setToolTipText(
1471 MessageManager.getString("label.toggle_sequence_visibility"));
1472 hideSelSequences.addActionListener(new ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 hideSelSequences_actionPerformed(e);
1480 JMenuItem hideSelColumns = new JMenuItem(
1481 MessageManager.getString("label.selected_columns"));
1482 hideSelColumns.setToolTipText(
1483 MessageManager.getString("label.toggle_columns_visibility"));
1484 hideSelColumns.addActionListener(new ActionListener()
1487 public void actionPerformed(ActionEvent e)
1489 hideSelColumns_actionPerformed(e);
1492 JMenuItem hideAllSelection = new JMenuItem(
1493 MessageManager.getString("label.selected_region"));
1494 hideAllSelection.addActionListener(new ActionListener()
1497 public void actionPerformed(ActionEvent e)
1499 hideAllSelection_actionPerformed(e);
1502 // TODO: should be hidden if no selection exists.
1503 JMenuItem hideAllButSelection = new JMenuItem(
1504 MessageManager.getString("label.all_but_selected_region"));
1505 hideAllButSelection.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 hideAllButSelection_actionPerformed(e);
1513 JMenuItem showAllhidden = new JMenuItem(
1514 MessageManager.getString("label.all_sequences_columns"));
1515 showAllhidden.setToolTipText(MessageManager
1516 .getString("label.toggles_visibility_hidden_selected_regions"));
1517 showAllhidden.addActionListener(new ActionListener()
1520 public void actionPerformed(ActionEvent e)
1522 showAllhidden_actionPerformed(e);
1525 hiddenMarkers.setText(
1526 MessageManager.getString("action.show_hidden_markers"));
1527 hiddenMarkers.addActionListener(new ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 hiddenMarkers_actionPerformed(e);
1536 JMenuItem invertColSel = new JMenuItem(
1537 MessageManager.getString("action.invert_column_selection"));
1538 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1539 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1540 | KeyEvent.ALT_MASK,
1542 al = new ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 invertColSel_actionPerformed(e);
1550 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1552 showComplementMenuItem.setVisible(false);
1553 showComplementMenuItem.addActionListener(new ActionListener()
1556 public void actionPerformed(ActionEvent e)
1558 showComplement_actionPerformed(showComplementMenuItem.getState());
1562 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1565 public void stateChanged(ChangeEvent evt)
1567 JTabbedPane pane = (JTabbedPane) evt.getSource();
1568 int sel = pane.getSelectedIndex();
1569 tabSelectionChanged(sel);
1572 tabbedPane.addMouseListener(new MouseAdapter()
1575 public void mousePressed(MouseEvent e)
1577 if (e.isPopupTrigger()) // Mac
1579 tabbedPane_mousePressed(e);
1584 public void mouseReleased(MouseEvent e)
1586 if (e.isPopupTrigger()) // Windows
1588 tabbedPane_mousePressed(e);
1592 tabbedPane.addFocusListener(new FocusAdapter()
1595 public void focusGained(FocusEvent e)
1597 tabbedPane_focusGained(e);
1601 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1602 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1603 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1604 al = new ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 save_actionPerformed(e);
1612 addMenuActionAndAccelerator(keyStroke, save, al);
1614 reload.setEnabled(false);
1615 reload.setText(MessageManager.getString("action.reload"));
1616 reload.addActionListener(new ActionListener()
1619 public void actionPerformed(ActionEvent e)
1621 reload_actionPerformed(e);
1625 JMenuItem newView = new JMenuItem(
1626 MessageManager.getString("action.new_view"));
1627 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1628 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1629 al = new ActionListener()
1632 public void actionPerformed(ActionEvent e)
1634 newView_actionPerformed(e);
1637 addMenuActionAndAccelerator(keyStroke, newView, al);
1639 tabbedPane.setToolTipText("<html><i>"
1640 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1643 formatMenu.setText(MessageManager.getString("action.format"));
1644 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1646 idRightAlign.setText(
1647 MessageManager.getString("label.right_align_sequence_id"));
1648 idRightAlign.addActionListener(new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 idRightAlign_actionPerformed(e);
1657 gatherViews.setEnabled(false);
1658 gatherViews.setText(MessageManager.getString("action.gather_views"));
1659 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1660 al = new ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 gatherViews_actionPerformed(e);
1668 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1670 expandViews.setEnabled(false);
1671 expandViews.setText(MessageManager.getString("action.expand_views"));
1672 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1673 al = new ActionListener()
1676 public void actionPerformed(ActionEvent e)
1678 expandViews_actionPerformed(e);
1681 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1683 JMenuItem pageSetup = new JMenuItem(
1684 MessageManager.getString("action.page_setup"));
1685 pageSetup.addActionListener(new ActionListener()
1688 public void actionPerformed(ActionEvent e)
1690 pageSetup_actionPerformed(e);
1693 JMenuItem alignmentProperties = new JMenuItem(
1694 MessageManager.getString("label.alignment_props"));
1695 alignmentProperties.addActionListener(new ActionListener()
1698 public void actionPerformed(ActionEvent actionEvent)
1700 alignmentProperties();
1703 JMenuItem selectHighlighted = new JMenuItem(
1704 MessageManager.getString("action.select_highlighted_columns"));
1705 selectHighlighted.setToolTipText(
1706 MessageManager.getString("tooltip.select_highlighted_columns"));
1707 al = new ActionListener()
1710 public void actionPerformed(ActionEvent actionEvent)
1712 selectHighlightedColumns_actionPerformed(actionEvent);
1715 selectHighlighted.addActionListener(al);
1716 JMenu tooltipSettingsMenu = new JMenu(
1717 MessageManager.getString("label.sequence_id_tooltip"));
1718 JMenu autoAnnMenu = new JMenu(
1719 MessageManager.getString("label.autocalculated_annotation"));
1721 JMenu exportImageMenu = new JMenu(
1722 MessageManager.getString("label.export_image"));
1723 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1724 alignFrameMenuBar.add(fileMenu);
1725 alignFrameMenuBar.add(editMenu);
1726 alignFrameMenuBar.add(selectMenu);
1727 alignFrameMenuBar.add(viewMenu);
1728 alignFrameMenuBar.add(annotationsMenu);
1729 alignFrameMenuBar.add(formatMenu);
1730 alignFrameMenuBar.add(colourMenu);
1731 alignFrameMenuBar.add(calculateMenu);
1732 alignFrameMenuBar.add(webService);
1734 fileMenu.add(fetchSequence);
1735 fileMenu.add(addSequenceMenu);
1736 fileMenu.add(reload);
1737 fileMenu.addSeparator();
1738 fileMenu.add(vamsasStore);
1740 fileMenu.add(saveAs);
1741 fileMenu.add(outputTextboxMenu);
1742 fileMenu.add(pageSetup);
1743 fileMenu.add(printMenuItem);
1744 fileMenu.addSeparator();
1745 fileMenu.add(exportImageMenu);
1746 fileMenu.add(exportFeatures);
1747 fileMenu.add(exportAnnotations);
1748 fileMenu.add(loadTreeMenuItem);
1749 fileMenu.add(associatedData);
1750 fileMenu.add(loadVcf);
1751 fileMenu.addSeparator();
1752 fileMenu.add(closeMenuItem);
1754 pasteMenu.add(pasteNew);
1755 pasteMenu.add(pasteThis);
1756 editMenu.add(undoMenuItem);
1757 editMenu.add(redoMenuItem);
1760 editMenu.add(pasteMenu);
1761 editMenu.add(delete);
1762 editMenu.addSeparator();
1763 editMenu.add(remove2LeftMenuItem);
1764 editMenu.add(remove2RightMenuItem);
1765 editMenu.add(removeGappedColumnMenuItem);
1766 editMenu.add(removeAllGapsMenuItem);
1767 editMenu.add(removeRedundancyMenuItem);
1768 editMenu.addSeparator();
1769 // dont add these yet in the CVS build - they cannot be undone!
1770 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1771 // editMenu.add(justifyLeftMenuItem);
1772 // editMenu.add(justifyRightMenuItem);
1773 // editMenu.addSeparator();
1774 editMenu.add(padGapsMenuitem);
1776 showMenu.add(showAllColumns);
1777 showMenu.add(showAllSeqs);
1778 showMenu.add(showAllhidden);
1779 hideMenu.add(hideSelColumns);
1780 hideMenu.add(hideSelSequences);
1781 hideMenu.add(hideAllSelection);
1782 hideMenu.add(hideAllButSelection);
1783 viewMenu.add(newView);
1784 viewMenu.add(expandViews);
1785 viewMenu.add(gatherViews);
1786 viewMenu.addSeparator();
1787 viewMenu.add(showMenu);
1788 viewMenu.add(hideMenu);
1789 viewMenu.add(showComplementMenuItem);
1790 viewMenu.addSeparator();
1791 viewMenu.add(followHighlightMenuItem);
1792 viewMenu.addSeparator();
1793 viewMenu.add(showSeqFeatures);
1794 // viewMenu.add(showSeqFeaturesHeight);
1795 viewMenu.add(openFeatureSettings);
1796 tooltipSettingsMenu.add(showDbRefsMenuitem);
1797 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1798 viewMenu.add(tooltipSettingsMenu);
1799 viewMenu.addSeparator();
1800 viewMenu.add(alignmentProperties);
1801 viewMenu.addSeparator();
1802 viewMenu.add(overviewMenuItem);
1804 annotationsMenu.add(annotationPanelMenuItem);
1805 annotationsMenu.addSeparator();
1806 annotationsMenu.add(showAllAlAnnotations);
1807 annotationsMenu.add(hideAllAlAnnotations);
1808 annotationsMenu.addSeparator();
1809 annotationsMenu.add(showAllSeqAnnotations);
1810 annotationsMenu.add(hideAllSeqAnnotations);
1811 annotationsMenu.add(sortAnnBySequence);
1812 annotationsMenu.add(sortAnnByLabel);
1813 annotationsMenu.addSeparator();
1814 autoAnnMenu.add(showAutoFirst);
1815 autoAnnMenu.add(showAutoLast);
1816 autoAnnMenu.addSeparator();
1817 autoAnnMenu.add(applyAutoAnnotationSettings);
1818 autoAnnMenu.add(showConsensusHistogram);
1819 autoAnnMenu.add(showSequenceLogo);
1820 autoAnnMenu.add(normaliseSequenceLogo);
1821 autoAnnMenu.addSeparator();
1822 autoAnnMenu.add(showGroupConservation);
1823 autoAnnMenu.add(showGroupConsensus);
1824 annotationsMenu.add(autoAnnMenu);
1826 sort.add(sortIDMenuItem);
1827 sort.add(sortLengthMenuItem);
1828 sort.add(sortGroupMenuItem);
1829 sort.add(sortPairwiseMenuItem);
1830 sort.add(sortByTreeMenu);
1831 calculateMenu.add(sort);
1832 calculateMenu.add(calculateTree);
1833 calculateMenu.addSeparator();
1834 calculateMenu.add(pairwiseAlignmentMenuItem);
1835 calculateMenu.addSeparator();
1836 calculateMenu.add(showTranslation);
1837 calculateMenu.add(showReverse);
1838 calculateMenu.add(showReverseComplement);
1839 calculateMenu.add(showProducts);
1840 calculateMenu.add(autoCalculate);
1841 calculateMenu.add(sortByTree);
1842 calculateMenu.addSeparator();
1843 calculateMenu.add(expandAlignment);
1844 calculateMenu.add(extractScores);
1845 calculateMenu.addSeparator();
1846 calculateMenu.add(runGroovy);
1848 webServiceNoServices = new JMenuItem(
1849 MessageManager.getString("label.no_services"));
1850 webService.add(webServiceNoServices);
1851 exportImageMenu.add(htmlMenuItem);
1852 exportImageMenu.add(epsFile);
1853 exportImageMenu.add(createPNG);
1854 exportImageMenu.add(createBioJS);
1855 exportImageMenu.add(createSVG);
1856 addSequenceMenu.add(addFromFile);
1857 addSequenceMenu.add(addFromText);
1858 addSequenceMenu.add(addFromURL);
1859 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1860 statusPanel.add(statusBar, null);
1861 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1863 formatMenu.add(font);
1864 formatMenu.addSeparator();
1865 formatMenu.add(wrapMenuItem);
1866 formatMenu.add(scaleAbove);
1867 formatMenu.add(scaleLeft);
1868 formatMenu.add(scaleRight);
1869 formatMenu.add(seqLimits);
1870 formatMenu.add(idRightAlign);
1871 formatMenu.add(hiddenMarkers);
1872 formatMenu.add(viewBoxesMenuItem);
1873 formatMenu.add(viewTextMenuItem);
1874 formatMenu.add(colourTextMenuItem);
1875 formatMenu.add(renderGapsMenuItem);
1876 formatMenu.add(centreColumnLabelsMenuItem);
1877 formatMenu.add(showNonconservedMenuItem);
1878 selectMenu.add(findMenuItem);
1879 selectMenu.addSeparator();
1880 selectMenu.add(selectAllSequenceMenuItem);
1881 selectMenu.add(deselectAllSequenceMenuItem);
1882 selectMenu.add(invertSequenceMenuItem);
1883 selectMenu.add(invertColSel);
1884 selectMenu.add(createGroup);
1885 selectMenu.add(unGroup);
1886 selectMenu.add(grpsFromSelection);
1887 selectMenu.add(deleteGroups);
1888 selectMenu.add(annotationColumn);
1889 selectMenu.add(selectHighlighted);
1890 // TODO - determine if the listenToViewSelections button is needed : see bug
1892 // selectMenu.addSeparator();
1893 // selectMenu.add(listenToViewSelections);
1896 protected void loadVcf_actionPerformed()
1901 * Constructs the entries on the Colour menu (but does not add them to the
1904 protected void initColourMenu()
1906 applyToAllGroups = new JCheckBoxMenuItem(
1907 MessageManager.getString("label.apply_colour_to_all_groups"));
1908 applyToAllGroups.addActionListener(new ActionListener()
1911 public void actionPerformed(ActionEvent e)
1913 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1917 textColour = new JMenuItem(
1918 MessageManager.getString("label.text_colour"));
1919 textColour.addActionListener(new ActionListener()
1922 public void actionPerformed(ActionEvent e)
1924 textColour_actionPerformed();
1928 conservationMenuItem = new JCheckBoxMenuItem(
1929 MessageManager.getString("action.by_conservation"));
1930 conservationMenuItem.addActionListener(new ActionListener()
1933 public void actionPerformed(ActionEvent e)
1935 conservationMenuItem_actionPerformed(
1936 conservationMenuItem.isSelected());
1940 abovePIDThreshold = new JCheckBoxMenuItem(
1941 MessageManager.getString("label.above_identity_threshold"));
1942 abovePIDThreshold.addActionListener(new ActionListener()
1945 public void actionPerformed(ActionEvent e)
1947 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1950 modifyPID = new JMenuItem(
1951 MessageManager.getString("label.modify_identity_threshold"));
1952 modifyPID.addActionListener(new ActionListener()
1955 public void actionPerformed(ActionEvent e)
1957 modifyPID_actionPerformed();
1960 modifyConservation = new JMenuItem(MessageManager
1961 .getString("label.modify_conservation_threshold"));
1962 modifyConservation.addActionListener(new ActionListener()
1965 public void actionPerformed(ActionEvent e)
1967 modifyConservation_actionPerformed();
1971 annotationColour = new JRadioButtonMenuItem(
1972 MessageManager.getString("action.by_annotation"));
1973 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1974 annotationColour.addActionListener(new ActionListener()
1977 public void actionPerformed(ActionEvent e)
1979 annotationColour_actionPerformed();
1984 protected void selectHighlightedColumns_actionPerformed(
1985 ActionEvent actionEvent)
1987 // TODO Auto-generated method stub
1992 * Generate the reverse sequence (or reverse complement if the flag is true)
1993 * and add it to the alignment
1997 protected void showReverse_actionPerformed(boolean complement)
2002 * Try to run script in a Groovy console, having first ensured that this
2003 * alignframe is set as currentAlignFrame in Desktop
2005 protected void runGroovy_actionPerformed()
2011 * Adds the given action listener and key accelerator to the given menu item.
2012 * Also saves in a lookup table to support lookup of action by key stroke.
2016 * @param actionListener
2018 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2019 JMenuItem menuItem, ActionListener actionListener)
2021 menuItem.setAccelerator(keyStroke);
2022 accelerators.put(keyStroke, menuItem);
2023 menuItem.addActionListener(actionListener);
2027 * Action on clicking sort annotations by type.
2031 protected void sortAnnotations()
2036 * Action on clicking Show all annotations.
2038 * @param forSequences
2039 * update sequence-related annotations
2040 * @param forAlignment
2041 * update non-sequence-related annotations
2043 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2044 boolean forAlignment)
2046 setAnnotationsVisibility(true, forSequences, forAlignment);
2050 * Action on clicking Hide all annotations.
2052 * @param forSequences
2053 * update sequence-related annotations
2054 * @param forAlignment
2055 * update non-sequence-related annotations
2057 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2058 boolean forAlignment)
2060 setAnnotationsVisibility(false, forSequences, forAlignment);
2064 * Set the visibility of annotations to true or false. Can act on
2065 * sequence-related annotations, or alignment-related, or both.
2068 * @param forSequences
2069 * update sequence-related annotations
2070 * @param forAlignment
2071 * update non-sequence-related annotations
2073 protected void setAnnotationsVisibility(boolean visible,
2074 boolean forSequences, boolean forAlignment)
2079 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2081 // TODO Auto-generated method stub
2085 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2087 // TODO Auto-generated method stub
2091 protected void showAllhidden_actionPerformed(ActionEvent e)
2093 // TODO Auto-generated method stub
2097 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2099 // TODO Auto-generated method stub
2103 protected void hideAllSelection_actionPerformed(ActionEvent e)
2105 // TODO Auto-generated method stub
2109 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2111 // TODO Auto-generated method stub
2115 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2117 // TODO Auto-generated method stub
2121 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2123 // TODO Auto-generated method stub
2127 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2129 // TODO Auto-generated method stub
2133 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2135 // TODO Auto-generated method stub
2139 protected void showGroupConservation_actionPerformed(ActionEvent e)
2141 // TODO Auto-generated method stub
2145 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2147 // TODO Auto-generated method stub
2151 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2153 // TODO Auto-generated method stub
2157 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2159 // TODO Auto-generated method stub
2163 protected void followHighlight_actionPerformed()
2165 // TODO Auto-generated method stub
2169 protected void showNpFeats_actionPerformed(ActionEvent e)
2171 // TODO Auto-generated method stub
2175 protected void showDbRefs_actionPerformed(ActionEvent e)
2177 // TODO Auto-generated method stub
2181 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2185 protected void buildSortByAnnotationScoresMenu()
2189 protected void extractScores_actionPerformed(ActionEvent e)
2193 protected void outputText_actionPerformed(ActionEvent e)
2197 public void addFromFile_actionPerformed(ActionEvent e)
2202 public void addFromText_actionPerformed(ActionEvent e)
2207 public void addFromURL_actionPerformed(ActionEvent e)
2212 public void exportFeatures_actionPerformed(ActionEvent e)
2217 public void exportAnnotations_actionPerformed(ActionEvent e)
2222 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2226 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2231 protected void closeMenuItem_actionPerformed(boolean b)
2235 protected void redoMenuItem_actionPerformed(ActionEvent e)
2239 protected void undoMenuItem_actionPerformed(ActionEvent e)
2243 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2247 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2251 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2255 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2259 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2263 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2267 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2271 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2275 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2279 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2283 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2287 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2291 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2295 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2299 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2303 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2307 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2311 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2315 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2319 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2323 protected void conservationMenuItem_actionPerformed(boolean selected)
2327 protected void printMenuItem_actionPerformed(ActionEvent e)
2331 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2335 protected void findMenuItem_actionPerformed(ActionEvent e)
2339 protected void abovePIDThreshold_actionPerformed(boolean selected)
2343 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2347 protected void deleteGroups_actionPerformed(ActionEvent e)
2351 protected void createGroup_actionPerformed(ActionEvent e)
2355 protected void unGroup_actionPerformed(ActionEvent e)
2359 protected void copy_actionPerformed(ActionEvent e)
2363 protected void cut_actionPerformed(ActionEvent e)
2367 protected void delete_actionPerformed(ActionEvent e)
2371 protected void pasteNew_actionPerformed(ActionEvent e)
2375 protected void pasteThis_actionPerformed(ActionEvent e)
2379 protected void applyToAllGroups_actionPerformed(boolean selected)
2383 public void createPNG(java.io.File f)
2387 protected void font_actionPerformed(ActionEvent e)
2391 protected void seqLimit_actionPerformed(ActionEvent e)
2395 public void seqDBRef_actionPerformed(ActionEvent e)
2400 public void createEPS(java.io.File f)
2404 public void createSVG(java.io.File f)
2409 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2415 * Template method to handle the 'load T-Coffee scores' menu event.
2417 * Subclasses override this method to provide a custom action.
2422 protected void loadScores_actionPerformed(ActionEvent event)
2427 protected void jpred_actionPerformed(ActionEvent e)
2431 protected void scaleAbove_actionPerformed(ActionEvent e)
2435 protected void scaleLeft_actionPerformed(ActionEvent e)
2439 protected void scaleRight_actionPerformed(ActionEvent e)
2443 protected void modifyPID_actionPerformed()
2447 protected void modifyConservation_actionPerformed()
2451 protected void saveAs_actionPerformed(ActionEvent e)
2455 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2459 public void vamsasStore_actionPerformed(ActionEvent e)
2464 public void vamsasLoad_actionPerformed(ActionEvent e)
2469 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2474 public void featureSettings_actionPerformed(ActionEvent e)
2479 public void fetchSequence_actionPerformed(ActionEvent e)
2484 public void smoothFont_actionPerformed(ActionEvent e)
2489 public void annotationColour_actionPerformed()
2493 public void annotationColumn_actionPerformed(ActionEvent e)
2497 public void associatedData_actionPerformed(ActionEvent e)
2502 public void autoCalculate_actionPerformed(ActionEvent e)
2507 public void sortByTreeOption_actionPerformed(ActionEvent e)
2512 public void showAllSeqs_actionPerformed(ActionEvent e)
2517 public void showAllColumns_actionPerformed(ActionEvent e)
2522 public void hideSelSequences_actionPerformed(ActionEvent e)
2527 public void hideSelColumns_actionPerformed(ActionEvent e)
2532 public void hiddenMarkers_actionPerformed(ActionEvent e)
2537 public void findPdbId_actionPerformed(ActionEvent e)
2542 public void enterPdbId_actionPerformed(ActionEvent e)
2547 public void pdbFile_actionPerformed(ActionEvent e)
2552 public void invertColSel_actionPerformed(ActionEvent e)
2557 public void tabSelectionChanged(int sel)
2562 public void tabbedPane_mousePressed(MouseEvent e)
2567 public void tabbedPane_focusGained(FocusEvent e)
2572 public void save_actionPerformed(ActionEvent e)
2577 public void reload_actionPerformed(ActionEvent e)
2582 public void newView_actionPerformed(ActionEvent e)
2587 public void textColour_actionPerformed()
2592 public void idRightAlign_actionPerformed(ActionEvent e)
2597 public void expandViews_actionPerformed(ActionEvent e)
2602 public void gatherViews_actionPerformed(ActionEvent e)
2607 public void buildTreeSortMenu()
2612 public void pageSetup_actionPerformed(ActionEvent e)
2617 public void alignmentProperties()
2622 protected void expand_newalign(ActionEvent e)
2624 // TODO Auto-generated method stub
2629 * Sets the value of the flag for 'show autocalculated annotations above other
2630 * annotations'. Answers true if the value changed, else false.
2632 * @param showAutoCalculatedAbove
2635 protected boolean setShowAutoCalculatedAbove(
2636 boolean showAutoCalculatedAbove)
2641 public void setAnnotationSortOrder(
2642 SequenceAnnotationOrder annotationSortOrder)
2646 public Map<KeyStroke, JMenuItem> getAccelerators()
2648 return this.accelerators;
2652 * Returns the selected index of the tabbed pane, or -1 if none selected
2653 * (including the case where the tabbed pane has not been made visible).
2657 public int getTabIndex()
2659 return tabbedPane.getSelectedIndex();
2662 public JPanel getStatusPanel()
2668 * Sets a reference to the containing split frame. Also makes the 'toggle
2669 * split view' menu item visible and checked.
2673 public void setSplitFrame(SplitContainerI sf)
2675 this.splitFrame = sf;
2678 this.showComplementMenuItem.setVisible(true);
2679 this.showComplementMenuItem.setState(true);
2683 public SplitContainerI getSplitViewContainer()
2685 return this.splitFrame;
2688 protected void showComplement_actionPerformed(boolean complement)