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.api.SplitContainerI;
25 import jalview.bin.Cache;
26 import jalview.gui.JvSwingUtils;
27 import jalview.gui.Preferences;
28 import jalview.io.FileFormats;
29 import jalview.util.MessageManager;
30 import jalview.util.Platform;
32 import java.awt.BorderLayout;
33 import java.awt.Color;
34 import java.awt.GridLayout;
35 import java.awt.Toolkit;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.FocusAdapter;
39 import java.awt.event.FocusEvent;
40 import java.awt.event.KeyEvent;
41 import java.awt.event.MouseAdapter;
42 import java.awt.event.MouseEvent;
43 import java.util.HashMap;
46 import javax.swing.BorderFactory;
47 import javax.swing.ButtonGroup;
48 import javax.swing.JCheckBoxMenuItem;
49 import javax.swing.JInternalFrame;
50 import javax.swing.JLabel;
51 import javax.swing.JMenu;
52 import javax.swing.JMenuBar;
53 import javax.swing.JMenuItem;
54 import javax.swing.JPanel;
55 import javax.swing.JRadioButtonMenuItem;
56 import javax.swing.JTabbedPane;
57 import javax.swing.KeyStroke;
58 import javax.swing.event.ChangeEvent;
59 import javax.swing.event.MenuEvent;
60 import javax.swing.event.MenuListener;
62 public class GAlignFrame extends JInternalFrame
64 protected JMenuBar alignFrameMenuBar = new JMenuBar();
66 protected JMenuItem closeMenuItem = new JMenuItem();
68 protected JMenu webService = new JMenu();
70 protected JMenuItem webServiceNoServices;
72 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
74 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
76 protected JMenu sortByAnnotScore = new JMenu();
78 public JLabel statusBar = new JLabel();
80 protected JMenu outputTextboxMenu = new JMenu();
82 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
84 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
86 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
88 protected JMenuItem undoMenuItem = new JMenuItem();
90 protected JMenuItem redoMenuItem = new JMenuItem();
92 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
94 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
96 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
98 JMenuItem copy = new JMenuItem();
100 JMenuItem cut = new JMenuItem();
102 JMenu pasteMenu = new JMenu();
104 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
106 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
108 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
110 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
112 protected JCheckBoxMenuItem applyToAllGroups;
114 protected JMenu colourMenu = new JMenu();
116 protected JMenuItem textColour;
118 protected JCheckBoxMenuItem conservationMenuItem;
120 protected JMenuItem modifyConservation;
122 protected JCheckBoxMenuItem abovePIDThreshold;
124 protected JMenuItem modifyPID;
126 protected JMenuItem annotationColour;
128 protected JMenu sortByTreeMenu = new JMenu();
130 protected JMenu sort = new JMenu();
132 protected JMenuItem calculateTree = new JMenuItem();
134 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
136 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
138 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
140 protected JMenuItem showTranslation = new JMenuItem();
142 protected JMenuItem showReverse = new JMenuItem();
144 protected JMenuItem showReverseComplement = new JMenuItem();
146 protected JMenu showProducts = new JMenu();
148 protected JMenuItem runGroovy = new JMenuItem();
150 protected JMenuItem loadVcf;
152 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
154 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
156 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
158 protected JPanel statusPanel = new JPanel();
160 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
162 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
164 protected JMenuItem showAllAlAnnotations = new JMenuItem();
166 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
168 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
170 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
172 protected JTabbedPane tabbedPane = new JTabbedPane();
174 protected JMenuItem reload = new JMenuItem();
176 protected JMenu formatMenu = new JMenu();
178 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
180 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
182 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
184 protected JMenuItem gatherViews = new JMenuItem();
186 protected JMenuItem expandViews = new JMenuItem();
188 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
190 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
192 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
194 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
196 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
198 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
200 private SequenceAnnotationOrder annotationSortOrder;
202 private boolean showAutoCalculatedAbove = false;
204 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
206 private SplitContainerI splitFrame;
213 setJMenuBar(alignFrameMenuBar);
215 // dynamically fill save as menu with available formats
216 for (String ff : FileFormats.getInstance().getWritableFormats(true))
218 JMenuItem item = new JMenuItem(ff);
220 item.addActionListener(new ActionListener()
223 public void actionPerformed(ActionEvent e)
225 outputText_actionPerformed(e);
229 outputTextboxMenu.add(item);
231 } catch (Exception e)
233 System.err.println(e.toString());
236 if (!Platform.isAMac())
238 closeMenuItem.setMnemonic('C');
239 outputTextboxMenu.setMnemonic('T');
240 undoMenuItem.setMnemonic('Z');
241 redoMenuItem.setMnemonic('0');
242 copy.setMnemonic('C');
243 cut.setMnemonic('U');
244 pasteMenu.setMnemonic('P');
245 reload.setMnemonic('R');
249 private void jbInit() throws Exception
253 JMenuItem saveAs = new JMenuItem(
254 MessageManager.getString("action.save_as"));
255 ActionListener al = new ActionListener()
258 public void actionPerformed(ActionEvent e)
260 saveAs_actionPerformed(e);
264 // FIXME getDefaultToolkit throws an exception in Headless mode
265 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
266 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
267 | KeyEvent.SHIFT_MASK,
269 addMenuActionAndAccelerator(keyStroke, saveAs, al);
271 closeMenuItem.setText(MessageManager.getString("action.close"));
272 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
273 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
274 al = new ActionListener()
277 public void actionPerformed(ActionEvent e)
279 closeMenuItem_actionPerformed(false);
282 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
284 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
285 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
286 JMenu annotationsMenu = new JMenu(
287 MessageManager.getString("action.annotations"));
288 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
289 colourMenu.setText(MessageManager.getString("action.colour"));
290 JMenu calculateMenu = new JMenu(
291 MessageManager.getString("action.calculate"));
292 webService.setText(MessageManager.getString("action.web_service"));
293 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
294 MessageManager.getString("action.select_all"));
295 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
296 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
297 al = new ActionListener()
300 public void actionPerformed(ActionEvent e)
302 selectAllSequenceMenuItem_actionPerformed(e);
305 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
307 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
308 MessageManager.getString("action.deselect_all"));
309 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
310 al = new ActionListener()
313 public void actionPerformed(ActionEvent e)
315 deselectAllSequenceMenuItem_actionPerformed(e);
318 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
320 JMenuItem invertSequenceMenuItem = new JMenuItem(
321 MessageManager.getString("action.invert_sequence_selection"));
322 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
323 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
324 al = new ActionListener()
327 public void actionPerformed(ActionEvent e)
329 invertSequenceMenuItem_actionPerformed(e);
332 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
334 JMenuItem grpsFromSelection = new JMenuItem(
335 MessageManager.getString("action.make_groups_selection"));
336 grpsFromSelection.addActionListener(new ActionListener()
339 public void actionPerformed(ActionEvent e)
341 makeGrpsFromSelection_actionPerformed(e);
344 JMenuItem expandAlignment = new JMenuItem(
345 MessageManager.getString("action.view_flanking_regions"));
346 expandAlignment.setToolTipText(
347 MessageManager.getString("label.view_flanking_regions"));
348 expandAlignment.addActionListener(new ActionListener()
351 public void actionPerformed(ActionEvent e)
356 JMenuItem remove2LeftMenuItem = new JMenuItem(
357 MessageManager.getString("action.remove_left"));
358 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
359 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
360 al = new ActionListener()
363 public void actionPerformed(ActionEvent e)
365 remove2LeftMenuItem_actionPerformed(e);
368 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
370 JMenuItem remove2RightMenuItem = new JMenuItem(
371 MessageManager.getString("action.remove_right"));
372 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
373 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
374 al = new ActionListener()
377 public void actionPerformed(ActionEvent e)
379 remove2RightMenuItem_actionPerformed(e);
382 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
384 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
385 MessageManager.getString("action.remove_empty_columns"));
386 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
387 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
388 al = new ActionListener()
391 public void actionPerformed(ActionEvent e)
393 removeGappedColumnMenuItem_actionPerformed(e);
396 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
398 JMenuItem removeAllGapsMenuItem = new JMenuItem(
399 MessageManager.getString("action.remove_all_gaps"));
400 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
401 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
402 | KeyEvent.SHIFT_MASK,
404 al = new ActionListener()
407 public void actionPerformed(ActionEvent e)
409 removeAllGapsMenuItem_actionPerformed(e);
412 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
414 JMenuItem justifyLeftMenuItem = new JMenuItem(
415 MessageManager.getString("action.left_justify_alignment"));
416 justifyLeftMenuItem.addActionListener(new ActionListener()
419 public void actionPerformed(ActionEvent e)
421 justifyLeftMenuItem_actionPerformed(e);
424 JMenuItem justifyRightMenuItem = new JMenuItem(
425 MessageManager.getString("action.right_justify_alignment"));
426 justifyRightMenuItem.addActionListener(new ActionListener()
429 public void actionPerformed(ActionEvent e)
431 justifyRightMenuItem_actionPerformed(e);
434 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
435 viewBoxesMenuItem.setState(true);
436 viewBoxesMenuItem.addActionListener(new ActionListener()
439 public void actionPerformed(ActionEvent e)
441 viewBoxesMenuItem_actionPerformed(e);
444 viewTextMenuItem.setText(MessageManager.getString("action.text"));
445 viewTextMenuItem.setState(true);
446 viewTextMenuItem.addActionListener(new ActionListener()
449 public void actionPerformed(ActionEvent e)
451 viewTextMenuItem_actionPerformed(e);
454 showNonconservedMenuItem
455 .setText(MessageManager.getString("label.show_non_conserved"));
456 showNonconservedMenuItem.setState(false);
457 showNonconservedMenuItem.addActionListener(new ActionListener()
460 public void actionPerformed(ActionEvent e)
462 showUnconservedMenuItem_actionPerformed(e);
465 JMenuItem sortPairwiseMenuItem = new JMenuItem(
466 MessageManager.getString("action.by_pairwise_id"));
467 sortPairwiseMenuItem.addActionListener(new ActionListener()
470 public void actionPerformed(ActionEvent e)
472 sortPairwiseMenuItem_actionPerformed(e);
475 JMenuItem sortIDMenuItem = new JMenuItem(
476 MessageManager.getString("action.by_id"));
477 sortIDMenuItem.addActionListener(new ActionListener()
480 public void actionPerformed(ActionEvent e)
482 sortIDMenuItem_actionPerformed(e);
485 JMenuItem sortLengthMenuItem = new JMenuItem(
486 MessageManager.getString("action.by_length"));
487 sortLengthMenuItem.addActionListener(new ActionListener()
490 public void actionPerformed(ActionEvent e)
492 sortLengthMenuItem_actionPerformed(e);
495 JMenuItem sortGroupMenuItem = new JMenuItem(
496 MessageManager.getString("action.by_group"));
497 sortGroupMenuItem.addActionListener(new ActionListener()
500 public void actionPerformed(ActionEvent e)
502 sortGroupMenuItem_actionPerformed(e);
506 JMenuItem removeRedundancyMenuItem = new JMenuItem(
507 MessageManager.getString("action.remove_redundancy"));
508 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
509 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
510 al = new ActionListener()
513 public void actionPerformed(ActionEvent e)
515 removeRedundancyMenuItem_actionPerformed(e);
518 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
520 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
521 MessageManager.getString("action.pairwise_alignment"));
522 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
525 public void actionPerformed(ActionEvent e)
527 pairwiseAlignmentMenuItem_actionPerformed(e);
531 this.getContentPane().setLayout(new BorderLayout());
532 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
533 statusBar.setBackground(Color.white);
534 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
535 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
536 statusBar.setText(MessageManager.getString("label.status_bar"));
538 .setText(MessageManager.getString("label.out_to_textbox"));
540 annotationPanelMenuItem.setActionCommand("");
541 annotationPanelMenuItem
542 .setText(MessageManager.getString("label.show_annotations"));
543 annotationPanelMenuItem
544 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
545 annotationPanelMenuItem.addActionListener(new ActionListener()
548 public void actionPerformed(ActionEvent e)
550 annotationPanelMenuItem_actionPerformed(e);
553 showAllAlAnnotations.setText(
554 MessageManager.getString("label.show_all_al_annotations"));
555 final boolean isAnnotationPanelShown = annotationPanelMenuItem
557 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
558 showAllAlAnnotations.addActionListener(new ActionListener()
561 public void actionPerformed(ActionEvent e)
563 showAllAnnotations_actionPerformed(false, true);
566 hideAllAlAnnotations.setText(
567 MessageManager.getString("label.hide_all_al_annotations"));
568 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
569 hideAllAlAnnotations.addActionListener(new ActionListener()
572 public void actionPerformed(ActionEvent e)
574 hideAllAnnotations_actionPerformed(false, true);
577 showAllSeqAnnotations.setText(
578 MessageManager.getString("label.show_all_seq_annotations"));
579 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
580 showAllSeqAnnotations.addActionListener(new ActionListener()
583 public void actionPerformed(ActionEvent e)
585 showAllAnnotations_actionPerformed(true, false);
588 hideAllSeqAnnotations.setText(
589 MessageManager.getString("label.hide_all_seq_annotations"));
590 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
591 hideAllSeqAnnotations.addActionListener(new ActionListener()
594 public void actionPerformed(ActionEvent e)
596 hideAllAnnotations_actionPerformed(true, false);
599 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
600 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
601 SequenceAnnotationOrder.NONE.name()));
602 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
603 MessageManager.getString("label.sort_annotations_by_sequence"));
604 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
605 MessageManager.getString("label.sort_annotations_by_label"));
607 sortAnnBySequence.setSelected(
608 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
609 sortAnnBySequence.addActionListener(new ActionListener()
612 public void actionPerformed(ActionEvent e)
614 boolean newState = sortAnnBySequence.getState();
615 sortAnnByLabel.setSelected(false);
616 setAnnotationSortOrder(
617 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
618 : SequenceAnnotationOrder.NONE);
619 sortAnnotations_actionPerformed();
622 sortAnnByLabel.setSelected(
623 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
624 sortAnnByLabel.addActionListener(new ActionListener()
627 public void actionPerformed(ActionEvent e)
629 boolean newState = sortAnnByLabel.getState();
630 sortAnnBySequence.setSelected(false);
631 setAnnotationSortOrder(
632 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
633 : SequenceAnnotationOrder.NONE);
634 sortAnnotations_actionPerformed();
637 colourTextMenuItem = new JCheckBoxMenuItem(
638 MessageManager.getString("label.colour_text"));
639 colourTextMenuItem.addActionListener(new ActionListener()
642 public void actionPerformed(ActionEvent e)
644 colourTextMenuItem_actionPerformed(e);
648 JMenuItem htmlMenuItem = new JMenuItem(
649 MessageManager.getString("label.html"));
650 htmlMenuItem.addActionListener(new ActionListener()
653 public void actionPerformed(ActionEvent e)
655 htmlMenuItem_actionPerformed(e);
659 JMenuItem createBioJS = new JMenuItem(
660 MessageManager.getString("label.biojs_html_export"));
661 createBioJS.addActionListener(new java.awt.event.ActionListener()
664 public void actionPerformed(ActionEvent e)
666 bioJSMenuItem_actionPerformed(e);
670 JMenuItem overviewMenuItem = new JMenuItem(
671 MessageManager.getString("label.overview_window"));
672 overviewMenuItem.addActionListener(new ActionListener()
675 public void actionPerformed(ActionEvent e)
677 overviewMenuItem_actionPerformed(e);
681 undoMenuItem.setEnabled(false);
682 undoMenuItem.setText(MessageManager.getString("action.undo"));
683 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
684 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
685 al = new ActionListener()
688 public void actionPerformed(ActionEvent e)
690 undoMenuItem_actionPerformed(e);
693 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
695 redoMenuItem.setEnabled(false);
696 redoMenuItem.setText(MessageManager.getString("action.redo"));
697 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
698 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
699 al = new ActionListener()
702 public void actionPerformed(ActionEvent e)
704 redoMenuItem_actionPerformed(e);
707 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
709 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
710 wrapMenuItem.addActionListener(new ActionListener()
713 public void actionPerformed(ActionEvent e)
715 wrapMenuItem_actionPerformed(e);
719 JMenuItem printMenuItem = new JMenuItem(
720 MessageManager.getString("action.print"));
721 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
722 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
723 al = new ActionListener()
726 public void actionPerformed(ActionEvent e)
728 printMenuItem_actionPerformed(e);
731 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
734 .setText(MessageManager.getString("action.show_gaps"));
735 renderGapsMenuItem.setState(true);
736 renderGapsMenuItem.addActionListener(new ActionListener()
739 public void actionPerformed(ActionEvent e)
741 renderGapsMenuItem_actionPerformed(e);
745 JMenuItem findMenuItem = new JMenuItem(
746 MessageManager.getString("action.find"));
747 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
748 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
749 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
750 MessageManager.getString("label.find_tip")));
751 al = new ActionListener()
754 public void actionPerformed(ActionEvent e)
756 findMenuItem_actionPerformed(e);
759 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
761 showSeqFeatures.setText(
762 MessageManager.getString("label.show_sequence_features"));
763 showSeqFeatures.addActionListener(new ActionListener()
766 public void actionPerformed(ActionEvent actionEvent)
768 showSeqFeatures_actionPerformed(actionEvent);
772 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
773 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
774 * void actionPerformed(ActionEvent actionEvent) {
775 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
778 .setText(MessageManager.getString("label.show_database_refs"));
779 showDbRefsMenuitem.addActionListener(new ActionListener()
783 public void actionPerformed(ActionEvent e)
785 showDbRefs_actionPerformed(e);
789 showNpFeatsMenuitem.setText(
790 MessageManager.getString("label.show_non_positional_features"));
791 showNpFeatsMenuitem.addActionListener(new ActionListener()
795 public void actionPerformed(ActionEvent e)
797 showNpFeats_actionPerformed(e);
801 showGroupConservation
802 .setText(MessageManager.getString("label.group_conservation"));
803 showGroupConservation.addActionListener(new ActionListener()
807 public void actionPerformed(ActionEvent e)
809 showGroupConservation_actionPerformed(e);
815 .setText(MessageManager.getString("label.group_consensus"));
816 showGroupConsensus.addActionListener(new ActionListener()
820 public void actionPerformed(ActionEvent e)
822 showGroupConsensus_actionPerformed(e);
826 showConsensusHistogram.setText(
827 MessageManager.getString("label.show_consensus_histogram"));
828 showConsensusHistogram.addActionListener(new ActionListener()
832 public void actionPerformed(ActionEvent e)
834 showConsensusHistogram_actionPerformed(e);
839 .setText(MessageManager.getString("label.show_consensus_logo"));
840 showSequenceLogo.addActionListener(new ActionListener()
844 public void actionPerformed(ActionEvent e)
846 showSequenceLogo_actionPerformed(e);
850 normaliseSequenceLogo
851 .setText(MessageManager.getString("label.norm_consensus_logo"));
852 normaliseSequenceLogo.addActionListener(new ActionListener()
856 public void actionPerformed(ActionEvent e)
858 normaliseSequenceLogo_actionPerformed(e);
862 applyAutoAnnotationSettings
863 .setText(MessageManager.getString("label.apply_all_groups"));
864 applyAutoAnnotationSettings.setState(false);
865 applyAutoAnnotationSettings.setVisible(true);
866 applyAutoAnnotationSettings.addActionListener(new ActionListener()
869 public void actionPerformed(ActionEvent e)
871 applyAutoAnnotationSettings_actionPerformed(e);
875 ButtonGroup buttonGroup = new ButtonGroup();
876 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
877 MessageManager.getString("label.show_first"));
878 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
879 MessageManager.getString("label.show_last"));
880 buttonGroup.add(showAutoFirst);
881 buttonGroup.add(showAutoLast);
882 final boolean autoFirst = Cache
883 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
884 showAutoFirst.setSelected(autoFirst);
885 setShowAutoCalculatedAbove(autoFirst);
886 showAutoFirst.addActionListener(new ActionListener()
889 public void actionPerformed(ActionEvent e)
891 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
892 sortAnnotations_actionPerformed();
895 showAutoLast.setSelected(!showAutoFirst.isSelected());
896 showAutoLast.addActionListener(new ActionListener()
899 public void actionPerformed(ActionEvent e)
901 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
902 sortAnnotations_actionPerformed();
906 JMenuItem deleteGroups = new JMenuItem(
907 MessageManager.getString("action.undefine_groups"));
908 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
909 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
910 al = new ActionListener()
913 public void actionPerformed(ActionEvent e)
915 deleteGroups_actionPerformed(e);
918 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
920 JMenuItem annotationColumn = new JMenuItem(
921 MessageManager.getString("action.select_by_annotation"));
922 annotationColumn.addActionListener(new ActionListener()
925 public void actionPerformed(ActionEvent e)
927 annotationColumn_actionPerformed(e);
931 JMenuItem createGroup = new JMenuItem(
932 MessageManager.getString("action.create_group"));
933 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
934 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
935 al = new ActionListener()
938 public void actionPerformed(ActionEvent e)
940 createGroup_actionPerformed(e);
943 addMenuActionAndAccelerator(keyStroke, createGroup, al);
945 JMenuItem unGroup = new JMenuItem(
946 MessageManager.getString("action.remove_group"));
947 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
948 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
949 | KeyEvent.SHIFT_MASK,
951 al = new ActionListener()
954 public void actionPerformed(ActionEvent e)
956 unGroup_actionPerformed(e);
959 addMenuActionAndAccelerator(keyStroke, unGroup, al);
961 copy.setText(MessageManager.getString("action.copy"));
962 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
963 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
965 al = new ActionListener()
968 public void actionPerformed(ActionEvent e)
970 copy_actionPerformed(e);
973 addMenuActionAndAccelerator(keyStroke, copy, al);
975 cut.setText(MessageManager.getString("action.cut"));
976 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
977 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
978 al = new ActionListener()
981 public void actionPerformed(ActionEvent e)
983 cut_actionPerformed(e);
986 addMenuActionAndAccelerator(keyStroke, cut, al);
988 JMenuItem delete = new JMenuItem(
989 MessageManager.getString("action.delete"));
990 delete.addActionListener(new ActionListener()
993 public void actionPerformed(ActionEvent e)
995 delete_actionPerformed(e);
999 pasteMenu.setText(MessageManager.getString("action.paste"));
1000 JMenuItem pasteNew = new JMenuItem(
1001 MessageManager.getString("label.to_new_alignment"));
1002 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1003 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1004 | KeyEvent.SHIFT_MASK,
1006 al = new ActionListener()
1009 public void actionPerformed(ActionEvent e)
1011 pasteNew_actionPerformed(e);
1014 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1016 JMenuItem pasteThis = new JMenuItem(
1017 MessageManager.getString("label.to_this_alignment"));
1018 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1019 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1020 al = new ActionListener()
1023 public void actionPerformed(ActionEvent e)
1025 pasteThis_actionPerformed(e);
1028 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1030 JMenuItem createPNG = new JMenuItem("PNG");
1031 createPNG.addActionListener(new ActionListener()
1034 public void actionPerformed(ActionEvent e)
1039 createPNG.setActionCommand(
1040 MessageManager.getString("label.save_png_image"));
1042 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1043 font.addActionListener(new ActionListener()
1046 public void actionPerformed(ActionEvent e)
1048 font_actionPerformed(e);
1052 MessageManager.getString("label.show_sequence_limits"));
1053 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1054 seqLimits.addActionListener(new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 seqLimit_actionPerformed(e);
1062 JMenuItem epsFile = new JMenuItem("EPS");
1063 epsFile.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1072 JMenuItem createSVG = new JMenuItem("SVG");
1073 createSVG.addActionListener(new ActionListener()
1076 public void actionPerformed(ActionEvent e)
1082 JMenuItem loadTreeMenuItem = new JMenuItem(
1083 MessageManager.getString("label.load_associated_tree"));
1084 loadTreeMenuItem.setActionCommand(
1085 MessageManager.getString("label.load_tree_for_sequence_set"));
1086 loadTreeMenuItem.addActionListener(new ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 loadTreeMenuItem_actionPerformed(e);
1095 scaleAbove.setVisible(false);
1096 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1097 scaleAbove.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 scaleAbove_actionPerformed(e);
1105 scaleLeft.setVisible(false);
1106 scaleLeft.setSelected(true);
1107 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1108 scaleLeft.addActionListener(new ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 scaleLeft_actionPerformed(e);
1116 scaleRight.setVisible(false);
1117 scaleRight.setSelected(true);
1118 scaleRight.setText(MessageManager.getString("action.scale_right"));
1119 scaleRight.addActionListener(new ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 scaleRight_actionPerformed(e);
1127 centreColumnLabelsMenuItem.setVisible(true);
1128 centreColumnLabelsMenuItem.setState(false);
1129 centreColumnLabelsMenuItem.setText(
1130 MessageManager.getString("label.centre_column_labels"));
1131 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 centreColumnLabels_actionPerformed(e);
1139 followHighlightMenuItem.setVisible(true);
1140 followHighlightMenuItem.setState(true);
1141 followHighlightMenuItem
1142 .setText(MessageManager.getString("label.automatic_scrolling"));
1143 followHighlightMenuItem.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent e)
1149 followHighlight_actionPerformed();
1155 .setText(MessageManager.getString("action.by_tree_order"));
1156 sort.setText(MessageManager.getString("action.sort"));
1157 sort.addMenuListener(new MenuListener()
1160 public void menuSelected(MenuEvent e)
1162 buildTreeSortMenu();
1166 public void menuDeselected(MenuEvent e)
1171 public void menuCanceled(MenuEvent e)
1176 .setText(MessageManager.getString("label.sort_by_score"));
1177 sort.add(sortByAnnotScore);
1178 sort.addMenuListener(new javax.swing.event.MenuListener()
1182 public void menuCanceled(MenuEvent e)
1187 public void menuDeselected(MenuEvent e)
1192 public void menuSelected(MenuEvent e)
1194 buildSortByAnnotationScoresMenu();
1197 sortByAnnotScore.setVisible(false);
1200 .setText(MessageManager.getString("action.calculate_tree_pca"));
1202 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1204 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1205 padGapsMenuitem.addActionListener(new ActionListener()
1208 public void actionPerformed(ActionEvent e)
1210 padGapsMenuitem_actionPerformed(e);
1213 JMenuItem vamsasStore = new JMenuItem(
1214 MessageManager.getString("label.vamsas_store"));
1215 vamsasStore.setVisible(false);
1216 vamsasStore.addActionListener(new ActionListener()
1219 public void actionPerformed(ActionEvent e)
1221 vamsasStore_actionPerformed(e);
1225 .setText(MessageManager.getString("label.translate_cDNA"));
1226 showTranslation.addActionListener(new ActionListener()
1229 public void actionPerformed(ActionEvent e)
1231 showTranslation_actionPerformed(e);
1234 showReverse.setText(MessageManager.getString("label.reverse"));
1235 showReverse.addActionListener(new ActionListener()
1238 public void actionPerformed(ActionEvent e)
1240 showReverse_actionPerformed(false);
1243 showReverseComplement
1244 .setText(MessageManager.getString("label.reverse_complement"));
1245 showReverseComplement.addActionListener(new ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 showReverse_actionPerformed(true);
1254 JMenuItem extractScores = new JMenuItem(
1255 MessageManager.getString("label.extract_scores"));
1256 extractScores.addActionListener(new ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 extractScores_actionPerformed(e);
1264 extractScores.setVisible(true);
1265 // JBPNote: TODO: make gui for regex based score extraction
1267 // for show products actions see AlignFrame.canShowProducts
1268 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1270 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1271 runGroovy.setToolTipText(
1272 MessageManager.getString("label.run_groovy_tip"));
1273 runGroovy.addActionListener(new ActionListener()
1276 public void actionPerformed(ActionEvent e)
1278 runGroovy_actionPerformed();
1282 JMenuItem openFeatureSettings = new JMenuItem(
1283 MessageManager.getString("action.feature_settings"));
1284 openFeatureSettings.addActionListener(new ActionListener()
1287 public void actionPerformed(ActionEvent e)
1289 featureSettings_actionPerformed(e);
1292 JMenuItem fetchSequence = new JMenuItem(
1293 MessageManager.getString("label.fetch_sequences"));
1294 fetchSequence.addActionListener(new ActionListener()
1297 public void actionPerformed(ActionEvent e)
1299 fetchSequence_actionPerformed(e);
1303 JMenuItem associatedData = new JMenuItem(
1304 MessageManager.getString("label.load_features_annotations"));
1305 associatedData.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 associatedData_actionPerformed(e);
1313 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1314 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1315 loadVcf.addActionListener(new ActionListener()
1318 public void actionPerformed(ActionEvent e)
1320 loadVcf_actionPerformed();
1323 autoCalculate.setText(
1324 MessageManager.getString("label.autocalculate_consensus"));
1325 autoCalculate.setState(
1326 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1327 autoCalculate.addActionListener(new ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 autoCalculate_actionPerformed(e);
1336 MessageManager.getString("label.sort_alignment_new_tree"));
1337 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1338 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1340 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1341 sortByTree.addActionListener(new ActionListener()
1344 public void actionPerformed(ActionEvent e)
1346 sortByTreeOption_actionPerformed(e);
1350 listenToViewSelections.setText(
1351 MessageManager.getString("label.listen_for_selections"));
1352 listenToViewSelections
1353 .setToolTipText("<html>" + MessageManager.getString(
1354 "label.selections_mirror_selections_made_same_sequences_other_views"));
1355 listenToViewSelections.setState(false);
1356 listenToViewSelections.addActionListener(new ActionListener()
1359 public void actionPerformed(ActionEvent e)
1361 listenToViewSelections_actionPerformed(e);
1365 JMenu addSequenceMenu = new JMenu(
1366 MessageManager.getString("label.add_sequences"));
1367 JMenuItem addFromFile = new JMenuItem(
1368 MessageManager.getString("label.from_file"));
1369 addFromFile.addActionListener(new ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 addFromFile_actionPerformed(e);
1377 JMenuItem addFromText = new JMenuItem(
1378 MessageManager.getString("label.from_textbox"));
1379 addFromText.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 addFromText_actionPerformed(e);
1387 JMenuItem addFromURL = new JMenuItem(
1388 MessageManager.getString("label.from_url"));
1389 addFromURL.addActionListener(new ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 addFromURL_actionPerformed(e);
1397 JMenuItem exportFeatures = new JMenuItem(
1398 MessageManager.getString("label.export_features"));
1399 exportFeatures.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 exportFeatures_actionPerformed(e);
1407 JMenuItem exportAnnotations = new JMenuItem(
1408 MessageManager.getString("label.export_annotations"));
1409 exportAnnotations.addActionListener(new ActionListener()
1412 public void actionPerformed(ActionEvent e)
1414 exportAnnotations_actionPerformed(e);
1417 statusPanel.setLayout(new GridLayout());
1418 JMenuItem showAllSeqs = new JMenuItem(
1419 MessageManager.getString("label.all_sequences"));
1420 showAllSeqs.setToolTipText(
1421 MessageManager.getString("label.toggle_sequence_visibility"));
1422 showAllSeqs.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 showAllSeqs_actionPerformed(e);
1430 JMenuItem showAllColumns = new JMenuItem(
1431 MessageManager.getString("label.all_columns"));
1432 showAllColumns.setToolTipText(
1433 MessageManager.getString("label.toggle_columns_visibility"));
1434 showAllColumns.addActionListener(new ActionListener()
1437 public void actionPerformed(ActionEvent e)
1439 showAllColumns_actionPerformed(e);
1442 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1443 JMenuItem hideSelSequences = new JMenuItem(
1444 MessageManager.getString("label.selected_sequences"));
1445 hideSelSequences.setToolTipText(
1446 MessageManager.getString("label.toggle_sequence_visibility"));
1447 hideSelSequences.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 hideSelSequences_actionPerformed(e);
1455 JMenuItem hideSelColumns = new JMenuItem(
1456 MessageManager.getString("label.selected_columns"));
1457 hideSelColumns.setToolTipText(
1458 MessageManager.getString("label.toggle_columns_visibility"));
1459 hideSelColumns.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 hideSelColumns_actionPerformed(e);
1467 JMenuItem hideAllSelection = new JMenuItem(
1468 MessageManager.getString("label.selected_region"));
1469 hideAllSelection.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 hideAllSelection_actionPerformed(e);
1477 // TODO: should be hidden if no selection exists.
1478 JMenuItem hideAllButSelection = new JMenuItem(
1479 MessageManager.getString("label.all_but_selected_region"));
1480 hideAllButSelection.addActionListener(new ActionListener()
1483 public void actionPerformed(ActionEvent e)
1485 hideAllButSelection_actionPerformed(e);
1488 JMenuItem showAllhidden = new JMenuItem(
1489 MessageManager.getString("label.all_sequences_columns"));
1490 showAllhidden.setToolTipText(MessageManager
1491 .getString("label.toggles_visibility_hidden_selected_regions"));
1492 showAllhidden.addActionListener(new ActionListener()
1495 public void actionPerformed(ActionEvent e)
1497 showAllhidden_actionPerformed(e);
1500 hiddenMarkers.setText(
1501 MessageManager.getString("action.show_hidden_markers"));
1502 hiddenMarkers.addActionListener(new ActionListener()
1505 public void actionPerformed(ActionEvent e)
1507 hiddenMarkers_actionPerformed(e);
1511 JMenuItem invertColSel = new JMenuItem(
1512 MessageManager.getString("action.invert_column_selection"));
1513 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1514 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1515 | KeyEvent.ALT_MASK,
1517 al = new ActionListener()
1520 public void actionPerformed(ActionEvent e)
1522 invertColSel_actionPerformed(e);
1525 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1527 showComplementMenuItem.setVisible(false);
1528 showComplementMenuItem.addActionListener(new ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 showComplement_actionPerformed(showComplementMenuItem.getState());
1537 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1540 public void stateChanged(ChangeEvent evt)
1542 JTabbedPane pane = (JTabbedPane) evt.getSource();
1543 int sel = pane.getSelectedIndex();
1544 tabSelectionChanged(sel);
1547 tabbedPane.addMouseListener(new MouseAdapter()
1550 public void mousePressed(MouseEvent e)
1552 if (e.isPopupTrigger()) // Mac
1554 tabbedPane_mousePressed(e);
1559 public void mouseReleased(MouseEvent e)
1561 if (e.isPopupTrigger()) // Windows
1563 tabbedPane_mousePressed(e);
1567 tabbedPane.addFocusListener(new FocusAdapter()
1570 public void focusGained(FocusEvent e)
1572 tabbedPane_focusGained(e);
1576 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1577 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1578 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1579 al = new ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 save_actionPerformed(e);
1587 addMenuActionAndAccelerator(keyStroke, save, al);
1589 reload.setEnabled(false);
1590 reload.setText(MessageManager.getString("action.reload"));
1591 reload.addActionListener(new ActionListener()
1594 public void actionPerformed(ActionEvent e)
1596 reload_actionPerformed(e);
1600 JMenuItem newView = new JMenuItem(
1601 MessageManager.getString("action.new_view"));
1602 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1603 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1604 al = new ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 newView_actionPerformed(e);
1612 addMenuActionAndAccelerator(keyStroke, newView, al);
1614 tabbedPane.setToolTipText("<html><i>"
1615 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1618 formatMenu.setText(MessageManager.getString("action.format"));
1619 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1621 idRightAlign.setText(
1622 MessageManager.getString("label.right_align_sequence_id"));
1623 idRightAlign.addActionListener(new ActionListener()
1626 public void actionPerformed(ActionEvent e)
1628 idRightAlign_actionPerformed(e);
1632 gatherViews.setEnabled(false);
1633 gatherViews.setText(MessageManager.getString("action.gather_views"));
1634 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1635 al = new ActionListener()
1638 public void actionPerformed(ActionEvent e)
1640 gatherViews_actionPerformed(e);
1643 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1645 expandViews.setEnabled(false);
1646 expandViews.setText(MessageManager.getString("action.expand_views"));
1647 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1648 al = new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 expandViews_actionPerformed(e);
1656 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1658 JMenuItem pageSetup = new JMenuItem(
1659 MessageManager.getString("action.page_setup"));
1660 pageSetup.addActionListener(new ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 pageSetup_actionPerformed(e);
1668 JMenuItem alignmentProperties = new JMenuItem(
1669 MessageManager.getString("label.alignment_props"));
1670 alignmentProperties.addActionListener(new ActionListener()
1673 public void actionPerformed(ActionEvent actionEvent)
1675 alignmentProperties();
1678 JMenuItem selectHighlighted = new JMenuItem(
1679 MessageManager.getString("action.select_highlighted_columns"));
1680 selectHighlighted.setToolTipText(
1681 MessageManager.getString("tooltip.select_highlighted_columns"));
1682 al = new ActionListener()
1685 public void actionPerformed(ActionEvent actionEvent)
1687 selectHighlightedColumns_actionPerformed(actionEvent);
1690 selectHighlighted.addActionListener(al);
1691 JMenu tooltipSettingsMenu = new JMenu(
1692 MessageManager.getString("label.sequence_id_tooltip"));
1693 JMenu autoAnnMenu = new JMenu(
1694 MessageManager.getString("label.autocalculated_annotation"));
1696 JMenu exportImageMenu = new JMenu(
1697 MessageManager.getString("label.export_image"));
1698 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1699 alignFrameMenuBar.add(fileMenu);
1700 alignFrameMenuBar.add(editMenu);
1701 alignFrameMenuBar.add(selectMenu);
1702 alignFrameMenuBar.add(viewMenu);
1703 alignFrameMenuBar.add(annotationsMenu);
1704 alignFrameMenuBar.add(formatMenu);
1705 alignFrameMenuBar.add(colourMenu);
1706 alignFrameMenuBar.add(calculateMenu);
1707 alignFrameMenuBar.add(webService);
1709 fileMenu.add(fetchSequence);
1710 fileMenu.add(addSequenceMenu);
1711 fileMenu.add(reload);
1712 fileMenu.addSeparator();
1713 fileMenu.add(vamsasStore);
1715 fileMenu.add(saveAs);
1716 fileMenu.add(outputTextboxMenu);
1717 fileMenu.add(pageSetup);
1718 fileMenu.add(printMenuItem);
1719 fileMenu.addSeparator();
1720 fileMenu.add(exportImageMenu);
1721 fileMenu.add(exportFeatures);
1722 fileMenu.add(exportAnnotations);
1723 fileMenu.add(loadTreeMenuItem);
1724 fileMenu.add(associatedData);
1725 fileMenu.add(loadVcf);
1726 fileMenu.addSeparator();
1727 fileMenu.add(closeMenuItem);
1729 pasteMenu.add(pasteNew);
1730 pasteMenu.add(pasteThis);
1731 editMenu.add(undoMenuItem);
1732 editMenu.add(redoMenuItem);
1735 editMenu.add(pasteMenu);
1736 editMenu.add(delete);
1737 editMenu.addSeparator();
1738 editMenu.add(remove2LeftMenuItem);
1739 editMenu.add(remove2RightMenuItem);
1740 editMenu.add(removeGappedColumnMenuItem);
1741 editMenu.add(removeAllGapsMenuItem);
1742 editMenu.add(removeRedundancyMenuItem);
1743 editMenu.addSeparator();
1744 // dont add these yet in the CVS build - they cannot be undone!
1745 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1746 // editMenu.add(justifyLeftMenuItem);
1747 // editMenu.add(justifyRightMenuItem);
1748 // editMenu.addSeparator();
1749 editMenu.add(padGapsMenuitem);
1751 showMenu.add(showAllColumns);
1752 showMenu.add(showAllSeqs);
1753 showMenu.add(showAllhidden);
1754 hideMenu.add(hideSelColumns);
1755 hideMenu.add(hideSelSequences);
1756 hideMenu.add(hideAllSelection);
1757 hideMenu.add(hideAllButSelection);
1758 viewMenu.add(newView);
1759 viewMenu.add(expandViews);
1760 viewMenu.add(gatherViews);
1761 viewMenu.addSeparator();
1762 viewMenu.add(showMenu);
1763 viewMenu.add(hideMenu);
1764 viewMenu.add(showComplementMenuItem);
1765 viewMenu.addSeparator();
1766 viewMenu.add(followHighlightMenuItem);
1767 viewMenu.addSeparator();
1768 viewMenu.add(showSeqFeatures);
1769 // viewMenu.add(showSeqFeaturesHeight);
1770 viewMenu.add(openFeatureSettings);
1771 tooltipSettingsMenu.add(showDbRefsMenuitem);
1772 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1773 viewMenu.add(tooltipSettingsMenu);
1774 viewMenu.addSeparator();
1775 viewMenu.add(alignmentProperties);
1776 viewMenu.addSeparator();
1777 viewMenu.add(overviewMenuItem);
1779 annotationsMenu.add(annotationPanelMenuItem);
1780 annotationsMenu.addSeparator();
1781 annotationsMenu.add(showAllAlAnnotations);
1782 annotationsMenu.add(hideAllAlAnnotations);
1783 annotationsMenu.addSeparator();
1784 annotationsMenu.add(showAllSeqAnnotations);
1785 annotationsMenu.add(hideAllSeqAnnotations);
1786 annotationsMenu.add(sortAnnBySequence);
1787 annotationsMenu.add(sortAnnByLabel);
1788 annotationsMenu.addSeparator();
1789 autoAnnMenu.add(showAutoFirst);
1790 autoAnnMenu.add(showAutoLast);
1791 autoAnnMenu.addSeparator();
1792 autoAnnMenu.add(applyAutoAnnotationSettings);
1793 autoAnnMenu.add(showConsensusHistogram);
1794 autoAnnMenu.add(showSequenceLogo);
1795 autoAnnMenu.add(normaliseSequenceLogo);
1796 autoAnnMenu.addSeparator();
1797 autoAnnMenu.add(showGroupConservation);
1798 autoAnnMenu.add(showGroupConsensus);
1799 annotationsMenu.add(autoAnnMenu);
1801 sort.add(sortIDMenuItem);
1802 sort.add(sortLengthMenuItem);
1803 sort.add(sortGroupMenuItem);
1804 sort.add(sortPairwiseMenuItem);
1805 sort.add(sortByTreeMenu);
1806 calculateMenu.add(sort);
1807 calculateMenu.add(calculateTree);
1808 calculateMenu.addSeparator();
1809 calculateMenu.add(pairwiseAlignmentMenuItem);
1810 calculateMenu.addSeparator();
1811 calculateMenu.add(showTranslation);
1812 calculateMenu.add(showReverse);
1813 calculateMenu.add(showReverseComplement);
1814 calculateMenu.add(showProducts);
1815 calculateMenu.add(autoCalculate);
1816 calculateMenu.add(sortByTree);
1817 calculateMenu.addSeparator();
1818 calculateMenu.add(expandAlignment);
1819 calculateMenu.add(extractScores);
1820 calculateMenu.addSeparator();
1821 calculateMenu.add(runGroovy);
1823 webServiceNoServices = new JMenuItem(
1824 MessageManager.getString("label.no_services"));
1825 webService.add(webServiceNoServices);
1826 exportImageMenu.add(htmlMenuItem);
1827 exportImageMenu.add(epsFile);
1828 exportImageMenu.add(createPNG);
1829 exportImageMenu.add(createBioJS);
1830 exportImageMenu.add(createSVG);
1831 addSequenceMenu.add(addFromFile);
1832 addSequenceMenu.add(addFromText);
1833 addSequenceMenu.add(addFromURL);
1834 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1835 statusPanel.add(statusBar, null);
1836 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1838 formatMenu.add(font);
1839 formatMenu.addSeparator();
1840 formatMenu.add(wrapMenuItem);
1841 formatMenu.add(scaleAbove);
1842 formatMenu.add(scaleLeft);
1843 formatMenu.add(scaleRight);
1844 formatMenu.add(seqLimits);
1845 formatMenu.add(idRightAlign);
1846 formatMenu.add(hiddenMarkers);
1847 formatMenu.add(viewBoxesMenuItem);
1848 formatMenu.add(viewTextMenuItem);
1849 formatMenu.add(colourTextMenuItem);
1850 formatMenu.add(renderGapsMenuItem);
1851 formatMenu.add(centreColumnLabelsMenuItem);
1852 formatMenu.add(showNonconservedMenuItem);
1853 selectMenu.add(findMenuItem);
1854 selectMenu.addSeparator();
1855 selectMenu.add(selectAllSequenceMenuItem);
1856 selectMenu.add(deselectAllSequenceMenuItem);
1857 selectMenu.add(invertSequenceMenuItem);
1858 selectMenu.add(invertColSel);
1859 selectMenu.add(createGroup);
1860 selectMenu.add(unGroup);
1861 selectMenu.add(grpsFromSelection);
1862 selectMenu.add(deleteGroups);
1863 selectMenu.add(annotationColumn);
1864 selectMenu.add(selectHighlighted);
1865 // TODO - determine if the listenToViewSelections button is needed : see bug
1867 // selectMenu.addSeparator();
1868 // selectMenu.add(listenToViewSelections);
1871 protected void loadVcf_actionPerformed()
1876 * Constructs the entries on the Colour menu (but does not add them to the
1879 protected void initColourMenu()
1881 applyToAllGroups = new JCheckBoxMenuItem(
1882 MessageManager.getString("label.apply_colour_to_all_groups"));
1883 applyToAllGroups.addActionListener(new ActionListener()
1886 public void actionPerformed(ActionEvent e)
1888 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1892 textColour = new JMenuItem(
1893 MessageManager.getString("label.text_colour"));
1894 textColour.addActionListener(new ActionListener()
1897 public void actionPerformed(ActionEvent e)
1899 textColour_actionPerformed();
1903 conservationMenuItem = new JCheckBoxMenuItem(
1904 MessageManager.getString("action.by_conservation"));
1905 conservationMenuItem.addActionListener(new ActionListener()
1908 public void actionPerformed(ActionEvent e)
1910 conservationMenuItem_actionPerformed(
1911 conservationMenuItem.isSelected());
1915 abovePIDThreshold = new JCheckBoxMenuItem(
1916 MessageManager.getString("label.above_identity_threshold"));
1917 abovePIDThreshold.addActionListener(new ActionListener()
1920 public void actionPerformed(ActionEvent e)
1922 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1925 modifyPID = new JMenuItem(
1926 MessageManager.getString("label.modify_identity_threshold"));
1927 modifyPID.addActionListener(new ActionListener()
1930 public void actionPerformed(ActionEvent e)
1932 modifyPID_actionPerformed();
1935 modifyConservation = new JMenuItem(MessageManager
1936 .getString("label.modify_conservation_threshold"));
1937 modifyConservation.addActionListener(new ActionListener()
1940 public void actionPerformed(ActionEvent e)
1942 modifyConservation_actionPerformed();
1946 annotationColour = new JMenuItem(
1947 MessageManager.getString("action.by_annotation"));
1948 annotationColour.addActionListener(new ActionListener()
1951 public void actionPerformed(ActionEvent e)
1953 annotationColour_actionPerformed();
1958 protected void selectHighlightedColumns_actionPerformed(
1959 ActionEvent actionEvent)
1961 // TODO Auto-generated method stub
1966 * Generate the reverse sequence (or reverse complement if the flag is true)
1967 * and add it to the alignment
1971 protected void showReverse_actionPerformed(boolean complement)
1976 * Try to run script in a Groovy console, having first ensured that this
1977 * alignframe is set as currentAlignFrame in Desktop
1979 protected void runGroovy_actionPerformed()
1985 * Adds the given action listener and key accelerator to the given menu item.
1986 * Also saves in a lookup table to support lookup of action by key stroke.
1990 * @param actionListener
1992 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
1993 JMenuItem menuItem, ActionListener actionListener)
1995 menuItem.setAccelerator(keyStroke);
1996 accelerators.put(keyStroke, menuItem);
1997 menuItem.addActionListener(actionListener);
2001 * Action on clicking sort annotations by type.
2005 protected void sortAnnotations_actionPerformed()
2010 * Action on clicking Show all annotations.
2012 * @param forSequences
2013 * update sequence-related annotations
2014 * @param forAlignment
2015 * update non-sequence-related annotations
2017 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2018 boolean forAlignment)
2020 setAnnotationsVisibility(true, forSequences, forAlignment);
2024 * Action on clicking Hide all annotations.
2026 * @param forSequences
2027 * update sequence-related annotations
2028 * @param forAlignment
2029 * update non-sequence-related annotations
2031 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2032 boolean forAlignment)
2034 setAnnotationsVisibility(false, forSequences, forAlignment);
2038 * Set the visibility of annotations to true or false. Can act on
2039 * sequence-related annotations, or alignment-related, or both.
2042 * @param forSequences
2043 * update sequence-related annotations
2044 * @param forAlignment
2045 * update non-sequence-related annotations
2047 protected void setAnnotationsVisibility(boolean visible,
2048 boolean forSequences, boolean forAlignment)
2053 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2055 // TODO Auto-generated method stub
2059 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2061 // TODO Auto-generated method stub
2065 protected void showAllhidden_actionPerformed(ActionEvent e)
2067 // TODO Auto-generated method stub
2071 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2073 // TODO Auto-generated method stub
2077 protected void hideAllSelection_actionPerformed(ActionEvent e)
2079 // TODO Auto-generated method stub
2083 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2085 // TODO Auto-generated method stub
2089 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2091 // TODO Auto-generated method stub
2095 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2097 // TODO Auto-generated method stub
2101 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2103 // TODO Auto-generated method stub
2107 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2109 // TODO Auto-generated method stub
2113 protected void showGroupConservation_actionPerformed(ActionEvent e)
2115 // TODO Auto-generated method stub
2119 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2121 // TODO Auto-generated method stub
2125 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2127 // TODO Auto-generated method stub
2131 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2133 // TODO Auto-generated method stub
2137 protected void followHighlight_actionPerformed()
2139 // TODO Auto-generated method stub
2143 protected void showNpFeats_actionPerformed(ActionEvent e)
2145 // TODO Auto-generated method stub
2149 protected void showDbRefs_actionPerformed(ActionEvent e)
2151 // TODO Auto-generated method stub
2155 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2159 protected void buildSortByAnnotationScoresMenu()
2163 protected void extractScores_actionPerformed(ActionEvent e)
2167 protected void outputText_actionPerformed(ActionEvent e)
2171 public void addFromFile_actionPerformed(ActionEvent e)
2176 public void addFromText_actionPerformed(ActionEvent e)
2181 public void addFromURL_actionPerformed(ActionEvent e)
2186 public void exportFeatures_actionPerformed(ActionEvent e)
2191 public void exportAnnotations_actionPerformed(ActionEvent e)
2196 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2200 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2205 protected void closeMenuItem_actionPerformed(boolean b)
2209 protected void redoMenuItem_actionPerformed(ActionEvent e)
2213 protected void undoMenuItem_actionPerformed(ActionEvent e)
2217 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2221 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2225 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2229 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2233 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2237 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2241 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2245 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2249 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2253 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2257 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2261 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2265 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2269 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2273 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2277 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2281 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2285 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2289 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2293 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2297 protected void conservationMenuItem_actionPerformed(boolean selected)
2301 protected void printMenuItem_actionPerformed(ActionEvent e)
2305 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2309 protected void findMenuItem_actionPerformed(ActionEvent e)
2313 protected void abovePIDThreshold_actionPerformed(boolean selected)
2317 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2321 protected void deleteGroups_actionPerformed(ActionEvent e)
2325 protected void createGroup_actionPerformed(ActionEvent e)
2329 protected void unGroup_actionPerformed(ActionEvent e)
2333 protected void copy_actionPerformed(ActionEvent e)
2337 protected void cut_actionPerformed(ActionEvent e)
2341 protected void delete_actionPerformed(ActionEvent e)
2345 protected void pasteNew_actionPerformed(ActionEvent e)
2349 protected void pasteThis_actionPerformed(ActionEvent e)
2353 protected void applyToAllGroups_actionPerformed(boolean selected)
2357 public void createPNG(java.io.File f)
2361 protected void font_actionPerformed(ActionEvent e)
2365 protected void seqLimit_actionPerformed(ActionEvent e)
2369 public void seqDBRef_actionPerformed(ActionEvent e)
2374 public void createEPS(java.io.File f)
2378 public void createSVG(java.io.File f)
2383 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2389 * Template method to handle the 'load T-Coffee scores' menu event.
2391 * Subclasses override this method to provide a custom action.
2396 protected void loadScores_actionPerformed(ActionEvent event)
2401 protected void jpred_actionPerformed(ActionEvent e)
2405 protected void scaleAbove_actionPerformed(ActionEvent e)
2409 protected void scaleLeft_actionPerformed(ActionEvent e)
2413 protected void scaleRight_actionPerformed(ActionEvent e)
2417 protected void modifyPID_actionPerformed()
2421 protected void modifyConservation_actionPerformed()
2425 protected void saveAs_actionPerformed(ActionEvent e)
2429 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2433 public void vamsasStore_actionPerformed(ActionEvent e)
2438 public void vamsasLoad_actionPerformed(ActionEvent e)
2443 public void showTranslation_actionPerformed(ActionEvent e)
2448 public void featureSettings_actionPerformed(ActionEvent e)
2453 public void fetchSequence_actionPerformed(ActionEvent e)
2458 public void smoothFont_actionPerformed(ActionEvent e)
2463 public void annotationColour_actionPerformed()
2467 public void annotationColumn_actionPerformed(ActionEvent e)
2471 public void associatedData_actionPerformed(ActionEvent e)
2476 public void autoCalculate_actionPerformed(ActionEvent e)
2481 public void sortByTreeOption_actionPerformed(ActionEvent e)
2486 public void showAllSeqs_actionPerformed(ActionEvent e)
2491 public void showAllColumns_actionPerformed(ActionEvent e)
2496 public void hideSelSequences_actionPerformed(ActionEvent e)
2501 public void hideSelColumns_actionPerformed(ActionEvent e)
2506 public void hiddenMarkers_actionPerformed(ActionEvent e)
2511 public void findPdbId_actionPerformed(ActionEvent e)
2516 public void enterPdbId_actionPerformed(ActionEvent e)
2521 public void pdbFile_actionPerformed(ActionEvent e)
2526 public void invertColSel_actionPerformed(ActionEvent e)
2531 public void tabSelectionChanged(int sel)
2536 public void tabbedPane_mousePressed(MouseEvent e)
2541 public void tabbedPane_focusGained(FocusEvent e)
2546 public void save_actionPerformed(ActionEvent e)
2551 public void reload_actionPerformed(ActionEvent e)
2556 public void newView_actionPerformed(ActionEvent e)
2561 public void textColour_actionPerformed()
2566 public void idRightAlign_actionPerformed(ActionEvent e)
2571 public void expandViews_actionPerformed(ActionEvent e)
2576 public void gatherViews_actionPerformed(ActionEvent e)
2581 public void buildTreeSortMenu()
2586 public void pageSetup_actionPerformed(ActionEvent e)
2591 public void alignmentProperties()
2596 protected void expand_newalign(ActionEvent e)
2598 // TODO Auto-generated method stub
2602 protected boolean isShowAutoCalculatedAbove()
2604 return showAutoCalculatedAbove;
2607 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2609 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2612 protected SequenceAnnotationOrder getAnnotationSortOrder()
2614 return annotationSortOrder;
2617 protected void setAnnotationSortOrder(
2618 SequenceAnnotationOrder annotationSortOrder)
2620 this.annotationSortOrder = annotationSortOrder;
2623 public Map<KeyStroke, JMenuItem> getAccelerators()
2625 return this.accelerators;
2629 * Returns the selected index of the tabbed pane, or -1 if none selected
2630 * (including the case where the tabbed pane has not been made visible).
2634 public int getTabIndex()
2636 return tabbedPane.getSelectedIndex();
2639 public JPanel getStatusPanel()
2645 * Sets a reference to the containing split frame. Also makes the 'toggle
2646 * split view' menu item visible and checked.
2650 public void setSplitFrame(SplitContainerI sf)
2652 this.splitFrame = sf;
2655 this.showComplementMenuItem.setVisible(true);
2656 this.showComplementMenuItem.setState(true);
2660 public SplitContainerI getSplitViewContainer()
2662 return this.splitFrame;
2665 protected void showComplement_actionPerformed(boolean complement)