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.bin.Jalview;
27 import jalview.gui.JvSwingUtils;
28 import jalview.gui.Preferences;
29 import jalview.io.FileFormats;
30 import jalview.util.MessageManager;
31 import jalview.util.Platform;
33 import java.awt.BorderLayout;
34 import java.awt.Color;
35 import java.awt.GridLayout;
36 import java.awt.Toolkit;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.event.FocusAdapter;
40 import java.awt.event.FocusEvent;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.MouseAdapter;
43 import java.awt.event.MouseEvent;
44 import java.util.HashMap;
47 import javax.swing.BorderFactory;
48 import javax.swing.ButtonGroup;
49 import javax.swing.JCheckBoxMenuItem;
50 import javax.swing.JInternalFrame;
51 import javax.swing.JLabel;
52 import javax.swing.JMenu;
53 import javax.swing.JMenuBar;
54 import javax.swing.JMenuItem;
55 import javax.swing.JPanel;
56 import javax.swing.JRadioButtonMenuItem;
57 import javax.swing.JTabbedPane;
58 import javax.swing.KeyStroke;
59 import javax.swing.event.ChangeEvent;
60 import javax.swing.event.MenuEvent;
61 import javax.swing.event.MenuListener;
63 public class GAlignFrame extends JInternalFrame
65 protected JMenuBar alignFrameMenuBar = new JMenuBar();
67 protected JMenuItem closeMenuItem = new JMenuItem();
69 protected JMenu webService = new JMenu();
71 protected JMenuItem webServiceNoServices;
73 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
75 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
77 protected JMenu sortByAnnotScore = new JMenu();
79 public JLabel statusBar = new JLabel();
81 protected JMenu outputTextboxMenu = new JMenu();
83 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
85 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
87 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
89 protected JMenuItem undoMenuItem = new JMenuItem();
91 protected JMenuItem redoMenuItem = new JMenuItem();
93 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
95 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
97 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
99 JMenuItem copy = new JMenuItem();
101 JMenuItem cut = new JMenuItem();
103 JMenu pasteMenu = new JMenu();
105 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
107 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
109 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
111 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
113 protected JCheckBoxMenuItem applyToAllGroups;
115 protected JMenu colourMenu = new JMenu();
117 protected JMenuItem textColour;
119 protected JCheckBoxMenuItem conservationMenuItem;
121 protected JMenuItem modifyConservation;
123 protected JCheckBoxMenuItem abovePIDThreshold;
125 protected JMenuItem modifyPID;
127 protected JMenuItem annotationColour;
129 protected JMenu sortByTreeMenu = new JMenu();
131 protected JMenu sort = new JMenu();
133 protected JMenuItem calculateTree = new JMenuItem();
135 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
137 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
139 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
141 protected JMenuItem showTranslation = new JMenuItem();
143 protected JMenuItem showReverse = new JMenuItem();
145 protected JMenuItem showReverseComplement = new JMenuItem();
147 protected JMenu showProducts = new JMenu();
149 protected JMenuItem runGroovy = new JMenuItem();
151 protected JMenuItem loadVcf;
153 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
155 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
157 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
159 protected JPanel statusPanel = new JPanel();
161 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
163 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
165 protected JMenuItem showAllAlAnnotations = new JMenuItem();
167 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
169 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
171 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
173 protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
175 protected JMenuItem reload = new JMenuItem();
177 protected JMenu formatMenu = new JMenu();
179 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
181 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
183 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
185 protected JMenuItem gatherViews = new JMenuItem();
187 protected JMenuItem expandViews = new JMenuItem();
189 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
191 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
193 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
201 protected JMenuItem openFeatureSettings;
203 private SequenceAnnotationOrder annotationSortOrder;
205 private boolean showAutoCalculatedAbove = false;
207 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
209 private SplitContainerI splitFrame;
216 setJMenuBar(alignFrameMenuBar);
218 // dynamically fill save as menu with available formats
219 for (String ff : FileFormats.getInstance().getWritableFormats(true))
221 JMenuItem item = new JMenuItem(ff);
223 item.addActionListener(new ActionListener()
226 public void actionPerformed(ActionEvent e)
228 outputText_actionPerformed(e.getActionCommand());
232 outputTextboxMenu.add(item);
234 } catch (Exception e)
236 System.err.println(e.toString());
239 if (!Platform.isAMac())
241 closeMenuItem.setMnemonic('C');
242 outputTextboxMenu.setMnemonic('T');
243 undoMenuItem.setMnemonic('Z');
244 redoMenuItem.setMnemonic('0');
245 copy.setMnemonic('C');
246 cut.setMnemonic('U');
247 pasteMenu.setMnemonic('P');
248 reload.setMnemonic('R');
252 private void jbInit() throws Exception
256 JMenuItem saveAs = new JMenuItem(
257 MessageManager.getString("action.save_as"));
258 ActionListener al = new ActionListener()
261 public void actionPerformed(ActionEvent e)
263 saveAs_actionPerformed();
267 // FIXME getDefaultToolkit throws an exception in Headless mode
268 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
269 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
270 | KeyEvent.SHIFT_MASK,
272 addMenuActionAndAccelerator(keyStroke, saveAs, al);
274 closeMenuItem.setText(MessageManager.getString("action.close"));
275 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
276 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
277 al = new ActionListener()
280 public void actionPerformed(ActionEvent e)
282 closeMenuItem_actionPerformed(false);
285 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
287 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
288 JMenu viewMenu = new JMenu(MessageManager.getString("action.view")) {
290 public void setPopupMenuVisible(boolean b) {
292 openFeatureSettings.setEnabled(haveAlignmentFeatures());
294 super.setPopupMenuVisible(b);
298 JMenu annotationsMenu = new JMenu(
299 MessageManager.getString("action.annotations"));
300 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
301 colourMenu.setText(MessageManager.getString("action.colour"));
302 JMenu calculateMenu = new JMenu(
303 MessageManager.getString("action.calculate"));
304 webService.setText(MessageManager.getString("action.web_service"));
305 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
306 MessageManager.getString("action.select_all"));
307 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
308 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
309 al = new ActionListener()
312 public void actionPerformed(ActionEvent e)
314 selectAllSequenceMenuItem_actionPerformed(e);
317 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
319 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
320 MessageManager.getString("action.deselect_all"));
321 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
322 al = new ActionListener()
325 public void actionPerformed(ActionEvent e)
327 deselectAllSequenceMenuItem_actionPerformed(e);
330 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
332 JMenuItem invertSequenceMenuItem = new JMenuItem(
333 MessageManager.getString("action.invert_sequence_selection"));
334 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
335 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
336 al = new ActionListener()
339 public void actionPerformed(ActionEvent e)
341 invertSequenceMenuItem_actionPerformed(e);
344 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
346 JMenuItem grpsFromSelection = new JMenuItem(
347 MessageManager.getString("action.make_groups_selection"));
348 grpsFromSelection.addActionListener(new ActionListener()
351 public void actionPerformed(ActionEvent e)
353 makeGrpsFromSelection_actionPerformed(e);
356 JMenuItem expandAlignment = new JMenuItem(
357 MessageManager.getString("action.view_flanking_regions"));
358 expandAlignment.setToolTipText(
359 MessageManager.getString("label.view_flanking_regions"));
360 expandAlignment.addActionListener(new ActionListener()
363 public void actionPerformed(ActionEvent e)
368 JMenuItem remove2LeftMenuItem = new JMenuItem(
369 MessageManager.getString("action.remove_left"));
370 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
371 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
372 al = new ActionListener()
375 public void actionPerformed(ActionEvent e)
377 remove2LeftMenuItem_actionPerformed(e);
380 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
382 JMenuItem remove2RightMenuItem = new JMenuItem(
383 MessageManager.getString("action.remove_right"));
384 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
385 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
386 al = new ActionListener()
389 public void actionPerformed(ActionEvent e)
391 remove2RightMenuItem_actionPerformed(e);
394 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
396 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
397 MessageManager.getString("action.remove_empty_columns"));
398 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
399 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
400 al = new ActionListener()
403 public void actionPerformed(ActionEvent e)
405 removeGappedColumnMenuItem_actionPerformed(e);
408 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
410 JMenuItem removeAllGapsMenuItem = new JMenuItem(
411 MessageManager.getString("action.remove_all_gaps"));
412 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
413 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
414 | KeyEvent.SHIFT_MASK,
416 al = new ActionListener()
419 public void actionPerformed(ActionEvent e)
421 removeAllGapsMenuItem_actionPerformed(e);
424 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
426 JMenuItem justifyLeftMenuItem = new JMenuItem(
427 MessageManager.getString("action.left_justify_alignment"));
428 justifyLeftMenuItem.addActionListener(new ActionListener()
431 public void actionPerformed(ActionEvent e)
433 justifyLeftMenuItem_actionPerformed(e);
436 JMenuItem justifyRightMenuItem = new JMenuItem(
437 MessageManager.getString("action.right_justify_alignment"));
438 justifyRightMenuItem.addActionListener(new ActionListener()
441 public void actionPerformed(ActionEvent e)
443 justifyRightMenuItem_actionPerformed(e);
446 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
447 viewBoxesMenuItem.setState(true);
448 viewBoxesMenuItem.addActionListener(new ActionListener()
451 public void actionPerformed(ActionEvent e)
453 viewBoxesMenuItem_actionPerformed(e);
456 viewTextMenuItem.setText(MessageManager.getString("action.text"));
457 viewTextMenuItem.setState(true);
458 viewTextMenuItem.addActionListener(new ActionListener()
461 public void actionPerformed(ActionEvent e)
463 viewTextMenuItem_actionPerformed(e);
466 showNonconservedMenuItem
467 .setText(MessageManager.getString("label.show_non_conserved"));
468 showNonconservedMenuItem.setState(false);
469 showNonconservedMenuItem.addActionListener(new ActionListener()
472 public void actionPerformed(ActionEvent e)
474 showUnconservedMenuItem_actionPerformed(e);
477 JMenuItem sortPairwiseMenuItem = new JMenuItem(
478 MessageManager.getString("action.by_pairwise_id"));
479 sortPairwiseMenuItem.addActionListener(new ActionListener()
482 public void actionPerformed(ActionEvent e)
484 sortPairwiseMenuItem_actionPerformed(e);
487 JMenuItem sortIDMenuItem = new JMenuItem(
488 MessageManager.getString("action.by_id"));
489 sortIDMenuItem.addActionListener(new ActionListener()
492 public void actionPerformed(ActionEvent e)
494 sortIDMenuItem_actionPerformed(e);
497 JMenuItem sortLengthMenuItem = new JMenuItem(
498 MessageManager.getString("action.by_length"));
499 sortLengthMenuItem.addActionListener(new ActionListener()
502 public void actionPerformed(ActionEvent e)
504 sortLengthMenuItem_actionPerformed(e);
507 JMenuItem sortGroupMenuItem = new JMenuItem(
508 MessageManager.getString("action.by_group"));
509 sortGroupMenuItem.addActionListener(new ActionListener()
512 public void actionPerformed(ActionEvent e)
514 sortGroupMenuItem_actionPerformed(e);
518 JMenuItem removeRedundancyMenuItem = new JMenuItem(
519 MessageManager.getString("action.remove_redundancy"));
520 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
521 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
522 al = new ActionListener()
525 public void actionPerformed(ActionEvent e)
527 removeRedundancyMenuItem_actionPerformed(e);
530 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
532 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
533 MessageManager.getString("action.pairwise_alignment"));
534 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
537 public void actionPerformed(ActionEvent e)
539 pairwiseAlignmentMenuItem_actionPerformed(e);
543 this.getContentPane().setLayout(new BorderLayout());
544 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
545 statusBar.setBackground(Color.white);
546 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
547 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
548 statusBar.setText(MessageManager.getString("label.status_bar"));
550 .setText(MessageManager.getString("label.out_to_textbox"));
552 annotationPanelMenuItem.setActionCommand("");
553 annotationPanelMenuItem
554 .setText(MessageManager.getString("label.show_annotations"));
555 annotationPanelMenuItem
556 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
557 annotationPanelMenuItem.addActionListener(new ActionListener()
560 public void actionPerformed(ActionEvent e)
562 annotationPanelMenuItem_actionPerformed(e);
565 showAllAlAnnotations.setText(
566 MessageManager.getString("label.show_all_al_annotations"));
567 final boolean isAnnotationPanelShown = annotationPanelMenuItem
569 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
570 showAllAlAnnotations.addActionListener(new ActionListener()
573 public void actionPerformed(ActionEvent e)
575 showAllAnnotations_actionPerformed(false, true);
578 hideAllAlAnnotations.setText(
579 MessageManager.getString("label.hide_all_al_annotations"));
580 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
581 hideAllAlAnnotations.addActionListener(new ActionListener()
584 public void actionPerformed(ActionEvent e)
586 hideAllAnnotations_actionPerformed(false, true);
589 showAllSeqAnnotations.setText(
590 MessageManager.getString("label.show_all_seq_annotations"));
591 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
592 showAllSeqAnnotations.addActionListener(new ActionListener()
595 public void actionPerformed(ActionEvent e)
597 showAllAnnotations_actionPerformed(true, false);
600 hideAllSeqAnnotations.setText(
601 MessageManager.getString("label.hide_all_seq_annotations"));
602 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
603 hideAllSeqAnnotations.addActionListener(new ActionListener()
606 public void actionPerformed(ActionEvent e)
608 hideAllAnnotations_actionPerformed(true, false);
611 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
612 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
613 SequenceAnnotationOrder.NONE.name()));
614 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
615 MessageManager.getString("label.sort_annotations_by_sequence"));
616 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
617 MessageManager.getString("label.sort_annotations_by_label"));
619 sortAnnBySequence.setSelected(
620 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
621 sortAnnBySequence.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent e)
626 boolean newState = sortAnnBySequence.getState();
627 sortAnnByLabel.setSelected(false);
628 setAnnotationSortOrder(
629 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
630 : SequenceAnnotationOrder.NONE);
631 sortAnnotations_actionPerformed();
634 sortAnnByLabel.setSelected(
635 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
636 sortAnnByLabel.addActionListener(new ActionListener()
639 public void actionPerformed(ActionEvent e)
641 boolean newState = sortAnnByLabel.getState();
642 sortAnnBySequence.setSelected(false);
643 setAnnotationSortOrder(
644 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
645 : SequenceAnnotationOrder.NONE);
646 sortAnnotations_actionPerformed();
649 colourTextMenuItem = new JCheckBoxMenuItem(
650 MessageManager.getString("label.colour_text"));
651 colourTextMenuItem.addActionListener(new ActionListener()
654 public void actionPerformed(ActionEvent e)
656 colourTextMenuItem_actionPerformed(e);
660 JMenuItem htmlMenuItem = new JMenuItem(
661 MessageManager.getString("label.html"));
662 htmlMenuItem.addActionListener(new ActionListener()
665 public void actionPerformed(ActionEvent e)
667 htmlMenuItem_actionPerformed(e);
671 JMenuItem createBioJS = new JMenuItem(
672 MessageManager.getString("label.biojs_html_export"));
673 createBioJS.addActionListener(new java.awt.event.ActionListener()
676 public void actionPerformed(ActionEvent e)
678 bioJSMenuItem_actionPerformed(e);
682 JMenuItem overviewMenuItem = new JMenuItem(
683 MessageManager.getString("label.overview_window"));
684 overviewMenuItem.addActionListener(new ActionListener()
687 public void actionPerformed(ActionEvent e)
689 overviewMenuItem_actionPerformed(e);
693 undoMenuItem.setEnabled(false);
694 undoMenuItem.setText(MessageManager.getString("action.undo"));
695 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
696 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
697 al = new ActionListener()
700 public void actionPerformed(ActionEvent e)
702 undoMenuItem_actionPerformed(e);
705 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
707 redoMenuItem.setEnabled(false);
708 redoMenuItem.setText(MessageManager.getString("action.redo"));
709 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
710 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
711 al = new ActionListener()
714 public void actionPerformed(ActionEvent e)
716 redoMenuItem_actionPerformed(e);
719 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
721 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
722 wrapMenuItem.addActionListener(new ActionListener()
725 public void actionPerformed(ActionEvent e)
727 wrapMenuItem_actionPerformed(e);
731 JMenuItem printMenuItem = new JMenuItem(
732 MessageManager.getString("action.print"));
733 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
734 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
735 al = new ActionListener()
738 public void actionPerformed(ActionEvent e)
740 printMenuItem_actionPerformed(e);
743 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
746 .setText(MessageManager.getString("action.show_gaps"));
747 renderGapsMenuItem.setState(true);
748 renderGapsMenuItem.addActionListener(new ActionListener()
751 public void actionPerformed(ActionEvent e)
753 renderGapsMenuItem_actionPerformed(e);
757 JMenuItem findMenuItem = new JMenuItem(
758 MessageManager.getString("action.find"));
759 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
760 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
761 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
762 MessageManager.getString("label.find_tip")));
763 al = new ActionListener()
766 public void actionPerformed(ActionEvent e)
768 findMenuItem_actionPerformed(e);
771 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
773 showSeqFeatures.setText(
774 MessageManager.getString("label.show_sequence_features"));
775 showSeqFeatures.addActionListener(new ActionListener()
778 public void actionPerformed(ActionEvent actionEvent)
780 showSeqFeatures_actionPerformed(actionEvent);
784 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
785 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
786 * void actionPerformed(ActionEvent actionEvent) {
787 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
790 .setText(MessageManager.getString("label.show_database_refs"));
791 showDbRefsMenuitem.addActionListener(new ActionListener()
795 public void actionPerformed(ActionEvent e)
797 showDbRefs_actionPerformed(e);
801 showNpFeatsMenuitem.setText(
802 MessageManager.getString("label.show_non_positional_features"));
803 showNpFeatsMenuitem.addActionListener(new ActionListener()
807 public void actionPerformed(ActionEvent e)
809 showNpFeats_actionPerformed(e);
813 showGroupConservation
814 .setText(MessageManager.getString("label.group_conservation"));
815 showGroupConservation.addActionListener(new ActionListener()
819 public void actionPerformed(ActionEvent e)
821 showGroupConservation_actionPerformed(e);
827 .setText(MessageManager.getString("label.group_consensus"));
828 showGroupConsensus.addActionListener(new ActionListener()
832 public void actionPerformed(ActionEvent e)
834 showGroupConsensus_actionPerformed(e);
838 showConsensusHistogram.setText(
839 MessageManager.getString("label.show_consensus_histogram"));
840 showConsensusHistogram.addActionListener(new ActionListener()
844 public void actionPerformed(ActionEvent e)
846 showConsensusHistogram_actionPerformed(e);
851 .setText(MessageManager.getString("label.show_consensus_logo"));
852 showSequenceLogo.addActionListener(new ActionListener()
856 public void actionPerformed(ActionEvent e)
858 showSequenceLogo_actionPerformed(e);
862 normaliseSequenceLogo
863 .setText(MessageManager.getString("label.norm_consensus_logo"));
864 normaliseSequenceLogo.addActionListener(new ActionListener()
868 public void actionPerformed(ActionEvent e)
870 normaliseSequenceLogo_actionPerformed(e);
874 applyAutoAnnotationSettings
875 .setText(MessageManager.getString("label.apply_all_groups"));
876 applyAutoAnnotationSettings.setState(false);
877 applyAutoAnnotationSettings.setVisible(true);
878 applyAutoAnnotationSettings.addActionListener(new ActionListener()
881 public void actionPerformed(ActionEvent e)
883 applyAutoAnnotationSettings_actionPerformed(e);
887 ButtonGroup buttonGroup = new ButtonGroup();
888 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
889 MessageManager.getString("label.show_first"));
890 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
891 MessageManager.getString("label.show_last"));
892 buttonGroup.add(showAutoFirst);
893 buttonGroup.add(showAutoLast);
894 final boolean autoFirst = Cache
895 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
896 showAutoFirst.setSelected(autoFirst);
897 setShowAutoCalculatedAbove(autoFirst);
898 showAutoFirst.addActionListener(new ActionListener()
901 public void actionPerformed(ActionEvent e)
903 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
904 sortAnnotations_actionPerformed();
907 showAutoLast.setSelected(!showAutoFirst.isSelected());
908 showAutoLast.addActionListener(new ActionListener()
911 public void actionPerformed(ActionEvent e)
913 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
914 sortAnnotations_actionPerformed();
918 JMenuItem deleteGroups = new JMenuItem(
919 MessageManager.getString("action.undefine_groups"));
920 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
921 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
922 al = new ActionListener()
925 public void actionPerformed(ActionEvent e)
927 deleteGroups_actionPerformed(e);
930 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
932 JMenuItem annotationColumn = new JMenuItem(
933 MessageManager.getString("action.select_by_annotation"));
934 annotationColumn.addActionListener(new ActionListener()
937 public void actionPerformed(ActionEvent e)
939 annotationColumn_actionPerformed(e);
943 JMenuItem createGroup = new JMenuItem(
944 MessageManager.getString("action.create_group"));
945 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
946 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
947 al = new ActionListener()
950 public void actionPerformed(ActionEvent e)
952 createGroup_actionPerformed(e);
955 addMenuActionAndAccelerator(keyStroke, createGroup, al);
957 JMenuItem unGroup = new JMenuItem(
958 MessageManager.getString("action.remove_group"));
959 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
960 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
961 | KeyEvent.SHIFT_MASK,
963 al = new ActionListener()
966 public void actionPerformed(ActionEvent e)
968 unGroup_actionPerformed(e);
971 addMenuActionAndAccelerator(keyStroke, unGroup, al);
973 copy.setText(MessageManager.getString("action.copy"));
974 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
975 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
977 al = new ActionListener()
980 public void actionPerformed(ActionEvent e)
982 copy_actionPerformed(e);
985 addMenuActionAndAccelerator(keyStroke, copy, al);
987 cut.setText(MessageManager.getString("action.cut"));
988 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
989 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
990 al = new ActionListener()
993 public void actionPerformed(ActionEvent e)
995 cut_actionPerformed(e);
998 addMenuActionAndAccelerator(keyStroke, cut, al);
1000 JMenuItem delete = new JMenuItem(
1001 MessageManager.getString("action.delete"));
1002 delete.addActionListener(new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 delete_actionPerformed(e);
1011 pasteMenu.setText(MessageManager.getString("action.paste"));
1012 JMenuItem pasteNew = new JMenuItem(
1013 MessageManager.getString("label.to_new_alignment"));
1014 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1015 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1016 | KeyEvent.SHIFT_MASK,
1018 al = new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 pasteNew_actionPerformed(e);
1026 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1028 JMenuItem pasteThis = new JMenuItem(
1029 MessageManager.getString("label.to_this_alignment"));
1030 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1031 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1032 al = new ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 pasteThis_actionPerformed(e);
1040 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1042 JMenuItem createPNG = new JMenuItem("PNG");
1043 createPNG.addActionListener(new ActionListener()
1046 public void actionPerformed(ActionEvent e)
1051 createPNG.setActionCommand(
1052 MessageManager.getString("label.save_png_image"));
1054 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1055 font.addActionListener(new ActionListener()
1058 public void actionPerformed(ActionEvent e)
1060 font_actionPerformed(e);
1064 MessageManager.getString("label.show_sequence_limits"));
1065 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1066 seqLimits.addActionListener(new ActionListener()
1069 public void actionPerformed(ActionEvent e)
1071 seqLimit_actionPerformed(e);
1074 JMenuItem epsFile = new JMenuItem("EPS");
1075 epsFile.addActionListener(new ActionListener()
1078 public void actionPerformed(ActionEvent e)
1084 JMenuItem createSVG = new JMenuItem("SVG");
1085 createSVG.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1094 JMenuItem loadTreeMenuItem = new JMenuItem(
1095 MessageManager.getString("label.load_associated_tree"));
1096 loadTreeMenuItem.setActionCommand(
1097 MessageManager.getString("label.load_tree_for_sequence_set"));
1098 loadTreeMenuItem.addActionListener(new ActionListener()
1101 public void actionPerformed(ActionEvent e)
1103 loadTreeMenuItem_actionPerformed(e);
1107 scaleAbove.setVisible(false);
1108 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1109 scaleAbove.addActionListener(new ActionListener()
1112 public void actionPerformed(ActionEvent e)
1114 scaleAbove_actionPerformed(e);
1117 scaleLeft.setVisible(false);
1118 scaleLeft.setSelected(true);
1119 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1120 scaleLeft.addActionListener(new ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 scaleLeft_actionPerformed(e);
1128 scaleRight.setVisible(false);
1129 scaleRight.setSelected(true);
1130 scaleRight.setText(MessageManager.getString("action.scale_right"));
1131 scaleRight.addActionListener(new ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 scaleRight_actionPerformed(e);
1139 centreColumnLabelsMenuItem.setVisible(true);
1140 centreColumnLabelsMenuItem.setState(false);
1141 centreColumnLabelsMenuItem.setText(
1142 MessageManager.getString("label.centre_column_labels"));
1143 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 centreColumnLabels_actionPerformed(e);
1151 followHighlightMenuItem.setVisible(true);
1152 followHighlightMenuItem.setState(true);
1153 followHighlightMenuItem
1154 .setText(MessageManager.getString("label.automatic_scrolling"));
1155 followHighlightMenuItem.addActionListener(new ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 followHighlight_actionPerformed();
1167 .setText(MessageManager.getString("action.by_tree_order"));
1168 sort.setText(MessageManager.getString("action.sort"));
1169 sort.addMenuListener(new MenuListener()
1172 public void menuSelected(MenuEvent e)
1174 buildTreeSortMenu();
1178 public void menuDeselected(MenuEvent e)
1183 public void menuCanceled(MenuEvent e)
1188 .setText(MessageManager.getString("label.sort_by_score"));
1189 sort.add(sortByAnnotScore);
1190 sort.addMenuListener(new javax.swing.event.MenuListener()
1194 public void menuCanceled(MenuEvent e)
1199 public void menuDeselected(MenuEvent e)
1204 public void menuSelected(MenuEvent e)
1206 buildSortByAnnotationScoresMenu();
1209 sortByAnnotScore.setVisible(false);
1212 .setText(MessageManager.getString("action.calculate_tree_pca"));
1214 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1216 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1217 padGapsMenuitem.addActionListener(new ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 padGapsMenuitem_actionPerformed(e);
1225 JMenuItem vamsasStore = new JMenuItem(
1226 MessageManager.getString("label.vamsas_store"));
1227 vamsasStore.setVisible(false);
1228 vamsasStore.addActionListener(new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 vamsasStore_actionPerformed(e);
1237 .setText(MessageManager.getString("label.translate_cDNA"));
1238 showTranslation.addActionListener(new ActionListener()
1241 public void actionPerformed(ActionEvent e)
1243 showTranslation_actionPerformed(e);
1246 showReverse.setText(MessageManager.getString("label.reverse"));
1247 showReverse.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 showReverse_actionPerformed(false);
1255 showReverseComplement
1256 .setText(MessageManager.getString("label.reverse_complement"));
1257 showReverseComplement.addActionListener(new ActionListener()
1260 public void actionPerformed(ActionEvent e)
1262 showReverse_actionPerformed(true);
1266 JMenuItem extractScores = new JMenuItem(
1267 MessageManager.getString("label.extract_scores"));
1268 extractScores.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 extractScores_actionPerformed(e);
1276 extractScores.setVisible(true);
1277 // JBPNote: TODO: make gui for regex based score extraction
1279 // for show products actions see AlignFrame.canShowProducts
1280 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1282 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1283 runGroovy.setToolTipText(
1284 MessageManager.getString("label.run_groovy_tip"));
1285 runGroovy.addActionListener(new ActionListener()
1288 public void actionPerformed(ActionEvent e)
1290 runGroovy_actionPerformed();
1294 openFeatureSettings = new JMenuItem(
1295 MessageManager.getString("action.feature_settings"));
1296 openFeatureSettings.setEnabled(false);
1297 openFeatureSettings.addActionListener(new ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 featureSettings_actionPerformed(e);
1305 JMenuItem fetchSequence = new JMenuItem(
1306 MessageManager.getString("label.fetch_sequences"));
1307 fetchSequence.addActionListener(new ActionListener()
1310 public void actionPerformed(ActionEvent e)
1312 fetchSequence_actionPerformed(e);
1316 JMenuItem associatedData = new JMenuItem(
1317 MessageManager.getString("label.load_features_annotations"));
1318 associatedData.addActionListener(new ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 associatedData_actionPerformed(e);
1326 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1327 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1328 loadVcf.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 loadVcf_actionPerformed();
1336 autoCalculate.setText(
1337 MessageManager.getString("label.autocalculate_consensus"));
1338 autoCalculate.setState(
1339 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1340 autoCalculate.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 autoCalculate_actionPerformed(e);
1349 MessageManager.getString("label.sort_alignment_new_tree"));
1350 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1351 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1353 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1354 sortByTree.addActionListener(new ActionListener()
1357 public void actionPerformed(ActionEvent e)
1359 sortByTreeOption_actionPerformed(e);
1363 listenToViewSelections.setText(
1364 MessageManager.getString("label.listen_for_selections"));
1365 listenToViewSelections
1366 .setToolTipText("<html>" + MessageManager.getString(
1367 "label.selections_mirror_selections_made_same_sequences_other_views"));
1368 listenToViewSelections.setState(false);
1369 listenToViewSelections.addActionListener(new ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 listenToViewSelections_actionPerformed(e);
1378 JMenu addSequenceMenu = new JMenu(
1379 MessageManager.getString("label.add_sequences"));
1380 JMenuItem addFromFile = new JMenuItem(
1381 MessageManager.getString("label.from_file"));
1382 addFromFile.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 addFromFile_actionPerformed(e);
1390 JMenuItem addFromText = new JMenuItem(
1391 MessageManager.getString("label.from_textbox"));
1392 addFromText.addActionListener(new ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 addFromText_actionPerformed(e);
1400 JMenuItem addFromURL = new JMenuItem(
1401 MessageManager.getString("label.from_url"));
1402 addFromURL.addActionListener(new ActionListener()
1405 public void actionPerformed(ActionEvent e)
1407 addFromURL_actionPerformed(e);
1410 JMenuItem exportFeatures = new JMenuItem(
1411 MessageManager.getString("label.export_features"));
1412 exportFeatures.addActionListener(new ActionListener()
1415 public void actionPerformed(ActionEvent e)
1417 exportFeatures_actionPerformed(e);
1420 JMenuItem exportAnnotations = new JMenuItem(
1421 MessageManager.getString("label.export_annotations"));
1422 exportAnnotations.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 exportAnnotations_actionPerformed(e);
1430 statusPanel.setLayout(new GridLayout());
1431 JMenuItem showAllSeqs = new JMenuItem(
1432 MessageManager.getString("label.all_sequences"));
1433 showAllSeqs.setToolTipText(
1434 MessageManager.getString("label.toggle_sequence_visibility"));
1435 showAllSeqs.addActionListener(new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1440 showAllSeqs_actionPerformed(e);
1443 JMenuItem showAllColumns = new JMenuItem(
1444 MessageManager.getString("label.all_columns"));
1445 showAllColumns.setToolTipText(
1446 MessageManager.getString("label.toggle_columns_visibility"));
1447 showAllColumns.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 showAllColumns_actionPerformed(e);
1455 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1456 JMenuItem hideSelSequences = new JMenuItem(
1457 MessageManager.getString("label.selected_sequences"));
1458 hideSelSequences.setToolTipText(
1459 MessageManager.getString("label.toggle_sequence_visibility"));
1460 hideSelSequences.addActionListener(new ActionListener()
1463 public void actionPerformed(ActionEvent e)
1465 hideSelSequences_actionPerformed(e);
1468 JMenuItem hideSelColumns = new JMenuItem(
1469 MessageManager.getString("label.selected_columns"));
1470 hideSelColumns.setToolTipText(
1471 MessageManager.getString("label.toggle_columns_visibility"));
1472 hideSelColumns.addActionListener(new ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 hideSelColumns_actionPerformed(e);
1480 JMenuItem hideAllSelection = new JMenuItem(
1481 MessageManager.getString("label.selected_region"));
1482 hideAllSelection.addActionListener(new ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 hideAllSelection_actionPerformed(e);
1490 // TODO: should be hidden if no selection exists.
1491 JMenuItem hideAllButSelection = new JMenuItem(
1492 MessageManager.getString("label.all_but_selected_region"));
1493 hideAllButSelection.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 hideAllButSelection_actionPerformed(e);
1501 JMenuItem showAllhidden = new JMenuItem(
1502 MessageManager.getString("label.all_sequences_columns"));
1503 showAllhidden.setToolTipText(MessageManager
1504 .getString("label.toggles_visibility_hidden_selected_regions"));
1505 showAllhidden.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 showAllhidden_actionPerformed(e);
1513 hiddenMarkers.setText(
1514 MessageManager.getString("action.show_hidden_markers"));
1515 hiddenMarkers.addActionListener(new ActionListener()
1518 public void actionPerformed(ActionEvent e)
1520 hiddenMarkers_actionPerformed(e);
1524 JMenuItem invertColSel = new JMenuItem(
1525 MessageManager.getString("action.invert_column_selection"));
1526 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1527 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1528 | KeyEvent.ALT_MASK,
1530 al = new ActionListener()
1533 public void actionPerformed(ActionEvent e)
1535 invertColSel_actionPerformed(e);
1538 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1540 showComplementMenuItem.setVisible(false);
1541 showComplementMenuItem.addActionListener(new ActionListener()
1544 public void actionPerformed(ActionEvent e)
1546 showComplement_actionPerformed(showComplementMenuItem.getState());
1550 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1553 public void stateChanged(ChangeEvent evt)
1555 JTabbedPane pane = (JTabbedPane) evt.getSource();
1556 int sel = pane.getSelectedIndex();
1557 tabSelectionChanged(sel);
1560 tabbedPane.addMouseListener(new MouseAdapter()
1563 public void mousePressed(MouseEvent e)
1565 if (e.isPopupTrigger()) // Mac
1567 tabbedPane_mousePressed(e);
1572 public void mouseReleased(MouseEvent e)
1574 if (e.isPopupTrigger()) // Windows
1576 tabbedPane_mousePressed(e);
1580 tabbedPane.addFocusListener(new FocusAdapter()
1583 public void focusGained(FocusEvent e)
1585 tabbedPane_focusGained(e);
1589 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1590 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1591 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1592 al = new ActionListener()
1595 public void actionPerformed(ActionEvent e)
1597 save_actionPerformed(e);
1600 addMenuActionAndAccelerator(keyStroke, save, al);
1602 reload.setEnabled(false);
1603 reload.setText(MessageManager.getString("action.reload"));
1604 reload.addActionListener(new ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 reload_actionPerformed(e);
1613 JMenuItem newView = new JMenuItem(
1614 MessageManager.getString("action.new_view"));
1615 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1616 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1617 al = new ActionListener()
1620 public void actionPerformed(ActionEvent e)
1622 newView_actionPerformed(e);
1625 addMenuActionAndAccelerator(keyStroke, newView, al);
1627 tabbedPane.setToolTipText("<html><i>"
1628 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1631 formatMenu.setText(MessageManager.getString("action.format"));
1632 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1634 idRightAlign.setText(
1635 MessageManager.getString("label.right_align_sequence_id"));
1636 idRightAlign.addActionListener(new ActionListener()
1639 public void actionPerformed(ActionEvent e)
1641 idRightAlign_actionPerformed(e);
1645 gatherViews.setEnabled(false);
1646 gatherViews.setText(MessageManager.getString("action.gather_views"));
1647 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1648 al = new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 gatherViews_actionPerformed(e);
1656 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1658 expandViews.setEnabled(false);
1659 expandViews.setText(MessageManager.getString("action.expand_views"));
1660 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1661 al = new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 expandViews_actionPerformed(e);
1669 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1671 JMenuItem pageSetup = new JMenuItem(
1672 MessageManager.getString("action.page_setup"));
1673 pageSetup.addActionListener(new ActionListener()
1676 public void actionPerformed(ActionEvent e)
1678 pageSetup_actionPerformed(e);
1681 JMenuItem alignmentProperties = new JMenuItem(
1682 MessageManager.getString("label.alignment_props"));
1683 alignmentProperties.addActionListener(new ActionListener()
1686 public void actionPerformed(ActionEvent actionEvent)
1688 alignmentProperties();
1691 JMenuItem selectHighlighted = new JMenuItem(
1692 MessageManager.getString("action.select_highlighted_columns"));
1693 selectHighlighted.setToolTipText(
1694 MessageManager.getString("tooltip.select_highlighted_columns"));
1695 al = new ActionListener()
1698 public void actionPerformed(ActionEvent actionEvent)
1700 selectHighlightedColumns_actionPerformed(actionEvent);
1703 selectHighlighted.addActionListener(al);
1704 JMenu tooltipSettingsMenu = new JMenu(
1705 MessageManager.getString("label.sequence_id_tooltip"));
1706 JMenu autoAnnMenu = new JMenu(
1707 MessageManager.getString("label.autocalculated_annotation"));
1709 JMenu exportImageMenu = new JMenu(
1710 MessageManager.getString("label.export_image"));
1711 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1712 alignFrameMenuBar.add(fileMenu);
1713 alignFrameMenuBar.add(editMenu);
1714 alignFrameMenuBar.add(selectMenu);
1715 alignFrameMenuBar.add(viewMenu);
1716 alignFrameMenuBar.add(annotationsMenu);
1717 alignFrameMenuBar.add(formatMenu);
1718 alignFrameMenuBar.add(colourMenu);
1719 alignFrameMenuBar.add(calculateMenu);
1720 if (!Jalview.isJS())
1722 alignFrameMenuBar.add(webService);
1725 fileMenu.add(fetchSequence);
1726 fileMenu.add(addSequenceMenu);
1727 fileMenu.add(reload);
1728 fileMenu.addSeparator();
1729 fileMenu.add(vamsasStore);
1731 fileMenu.add(saveAs);
1732 fileMenu.add(outputTextboxMenu);
1733 fileMenu.add(pageSetup);
1734 fileMenu.add(printMenuItem);
1735 fileMenu.addSeparator();
1736 fileMenu.add(exportImageMenu);
1737 fileMenu.add(exportFeatures);
1738 fileMenu.add(exportAnnotations);
1739 fileMenu.add(loadTreeMenuItem);
1740 fileMenu.add(associatedData);
1741 if (!Jalview.isJS())
1743 fileMenu.add(loadVcf);
1745 fileMenu.addSeparator();
1746 fileMenu.add(closeMenuItem);
1748 pasteMenu.add(pasteNew);
1749 pasteMenu.add(pasteThis);
1750 editMenu.add(undoMenuItem);
1751 editMenu.add(redoMenuItem);
1754 editMenu.add(pasteMenu);
1755 editMenu.add(delete);
1756 editMenu.addSeparator();
1757 editMenu.add(remove2LeftMenuItem);
1758 editMenu.add(remove2RightMenuItem);
1759 editMenu.add(removeGappedColumnMenuItem);
1760 editMenu.add(removeAllGapsMenuItem);
1761 editMenu.add(removeRedundancyMenuItem);
1762 editMenu.addSeparator();
1763 // dont add these yet in the CVS build - they cannot be undone!
1764 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1765 // editMenu.add(justifyLeftMenuItem);
1766 // editMenu.add(justifyRightMenuItem);
1767 // editMenu.addSeparator();
1768 editMenu.add(padGapsMenuitem);
1770 showMenu.add(showAllColumns);
1771 showMenu.add(showAllSeqs);
1772 showMenu.add(showAllhidden);
1773 hideMenu.add(hideSelColumns);
1774 hideMenu.add(hideSelSequences);
1775 hideMenu.add(hideAllSelection);
1776 hideMenu.add(hideAllButSelection);
1777 viewMenu.add(newView);
1778 if (!Jalview.isJS())
1780 viewMenu.add(expandViews);
1781 viewMenu.add(gatherViews);
1783 viewMenu.addSeparator();
1784 viewMenu.add(showMenu);
1785 viewMenu.add(hideMenu);
1786 viewMenu.add(showComplementMenuItem);
1787 viewMenu.addSeparator();
1788 viewMenu.add(followHighlightMenuItem);
1789 viewMenu.addSeparator();
1790 viewMenu.add(showSeqFeatures);
1791 // viewMenu.add(showSeqFeaturesHeight);
1792 viewMenu.add(openFeatureSettings);
1793 tooltipSettingsMenu.add(showDbRefsMenuitem);
1794 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1795 viewMenu.add(tooltipSettingsMenu);
1796 viewMenu.addSeparator();
1797 viewMenu.add(alignmentProperties);
1798 viewMenu.addSeparator();
1799 viewMenu.add(overviewMenuItem);
1801 annotationsMenu.add(annotationPanelMenuItem);
1802 annotationsMenu.addSeparator();
1803 annotationsMenu.add(showAllAlAnnotations);
1804 annotationsMenu.add(hideAllAlAnnotations);
1805 annotationsMenu.addSeparator();
1806 annotationsMenu.add(showAllSeqAnnotations);
1807 annotationsMenu.add(hideAllSeqAnnotations);
1808 annotationsMenu.add(sortAnnBySequence);
1809 annotationsMenu.add(sortAnnByLabel);
1810 annotationsMenu.addSeparator();
1811 autoAnnMenu.add(showAutoFirst);
1812 autoAnnMenu.add(showAutoLast);
1813 autoAnnMenu.addSeparator();
1814 autoAnnMenu.add(applyAutoAnnotationSettings);
1815 autoAnnMenu.add(showConsensusHistogram);
1816 autoAnnMenu.add(showSequenceLogo);
1817 autoAnnMenu.add(normaliseSequenceLogo);
1818 autoAnnMenu.addSeparator();
1819 autoAnnMenu.add(showGroupConservation);
1820 autoAnnMenu.add(showGroupConsensus);
1821 annotationsMenu.add(autoAnnMenu);
1823 sort.add(sortIDMenuItem);
1824 sort.add(sortLengthMenuItem);
1825 sort.add(sortGroupMenuItem);
1826 sort.add(sortPairwiseMenuItem);
1827 sort.add(sortByTreeMenu);
1828 calculateMenu.add(sort);
1829 calculateMenu.add(calculateTree);
1830 calculateMenu.addSeparator();
1831 calculateMenu.add(pairwiseAlignmentMenuItem);
1832 calculateMenu.addSeparator();
1833 calculateMenu.add(showTranslation);
1834 calculateMenu.add(showReverse);
1835 calculateMenu.add(showReverseComplement);
1836 calculateMenu.add(showProducts);
1837 calculateMenu.add(autoCalculate);
1838 calculateMenu.add(sortByTree);
1839 calculateMenu.addSeparator();
1840 calculateMenu.add(expandAlignment);
1841 calculateMenu.add(extractScores);
1842 if (!Jalview.isJS())
1844 calculateMenu.addSeparator();
1845 calculateMenu.add(runGroovy);
1848 webServiceNoServices = new JMenuItem(
1849 MessageManager.getString("label.no_services"));
1850 webService.add(webServiceNoServices);
1851 if (!Jalview.isJS())
1853 exportImageMenu.add(htmlMenuItem);
1855 exportImageMenu.add(epsFile);
1856 exportImageMenu.add(createPNG);
1857 exportImageMenu.add(createBioJS);
1858 if (!Jalview.isJS())
1860 exportImageMenu.add(createSVG);
1862 addSequenceMenu.add(addFromFile);
1863 addSequenceMenu.add(addFromText);
1864 addSequenceMenu.add(addFromURL);
1865 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1866 statusPanel.add(statusBar, null);
1867 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1869 formatMenu.add(font);
1870 formatMenu.addSeparator();
1871 formatMenu.add(wrapMenuItem);
1872 formatMenu.add(scaleAbove);
1873 formatMenu.add(scaleLeft);
1874 formatMenu.add(scaleRight);
1875 formatMenu.add(seqLimits);
1876 formatMenu.add(idRightAlign);
1877 formatMenu.add(hiddenMarkers);
1878 formatMenu.add(viewBoxesMenuItem);
1879 formatMenu.add(viewTextMenuItem);
1880 formatMenu.add(colourTextMenuItem);
1881 formatMenu.add(renderGapsMenuItem);
1882 formatMenu.add(centreColumnLabelsMenuItem);
1883 formatMenu.add(showNonconservedMenuItem);
1884 selectMenu.add(findMenuItem);
1885 selectMenu.addSeparator();
1886 selectMenu.add(selectAllSequenceMenuItem);
1887 selectMenu.add(deselectAllSequenceMenuItem);
1888 selectMenu.add(invertSequenceMenuItem);
1889 selectMenu.add(invertColSel);
1890 selectMenu.add(createGroup);
1891 selectMenu.add(unGroup);
1892 selectMenu.add(grpsFromSelection);
1893 selectMenu.add(deleteGroups);
1894 selectMenu.add(annotationColumn);
1895 selectMenu.add(selectHighlighted);
1896 // TODO - determine if the listenToViewSelections button is needed : see bug
1898 // selectMenu.addSeparator();
1899 // selectMenu.add(listenToViewSelections);
1902 protected boolean haveAlignmentFeatures()
1904 // because gAlignFrame is not an abstract class -- see AlignFrame
1908 protected void loadVcf_actionPerformed()
1913 * Constructs the entries on the Colour menu (but does not add them to the
1916 protected void initColourMenu()
1918 applyToAllGroups = new JCheckBoxMenuItem(
1919 MessageManager.getString("label.apply_colour_to_all_groups"));
1920 applyToAllGroups.addActionListener(new ActionListener()
1923 public void actionPerformed(ActionEvent e)
1925 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1929 textColour = new JMenuItem(
1930 MessageManager.getString("label.text_colour"));
1931 textColour.addActionListener(new ActionListener()
1934 public void actionPerformed(ActionEvent e)
1936 textColour_actionPerformed();
1940 conservationMenuItem = new JCheckBoxMenuItem(
1941 MessageManager.getString("action.by_conservation"));
1942 conservationMenuItem.addActionListener(new ActionListener()
1945 public void actionPerformed(ActionEvent e)
1947 conservationMenuItem_actionPerformed(
1948 conservationMenuItem.isSelected());
1952 abovePIDThreshold = new JCheckBoxMenuItem(
1953 MessageManager.getString("label.above_identity_threshold"));
1954 abovePIDThreshold.addActionListener(new ActionListener()
1957 public void actionPerformed(ActionEvent e)
1959 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1962 modifyPID = new JMenuItem(
1963 MessageManager.getString("label.modify_identity_threshold"));
1964 modifyPID.addActionListener(new ActionListener()
1967 public void actionPerformed(ActionEvent e)
1969 modifyPID_actionPerformed();
1972 modifyConservation = new JMenuItem(MessageManager
1973 .getString("label.modify_conservation_threshold"));
1974 modifyConservation.addActionListener(new ActionListener()
1977 public void actionPerformed(ActionEvent e)
1979 modifyConservation_actionPerformed();
1983 annotationColour = new JMenuItem(
1984 MessageManager.getString("action.by_annotation"));
1985 annotationColour.addActionListener(new ActionListener()
1988 public void actionPerformed(ActionEvent e)
1990 annotationColour_actionPerformed();
1995 protected void selectHighlightedColumns_actionPerformed(
1996 ActionEvent actionEvent)
1998 // TODO Auto-generated method stub
2003 * Generate the reverse sequence (or reverse complement if the flag is true)
2004 * and add it to the alignment
2008 protected void showReverse_actionPerformed(boolean complement)
2013 * Try to run script in a Groovy console, having first ensured that this
2014 * alignframe is set as currentAlignFrame in Desktop
2016 protected void runGroovy_actionPerformed()
2022 * Adds the given action listener and key accelerator to the given menu item.
2023 * Also saves in a lookup table to support lookup of action by key stroke.
2027 * @param actionListener
2029 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2030 JMenuItem menuItem, ActionListener actionListener)
2032 menuItem.setAccelerator(keyStroke);
2033 accelerators.put(keyStroke, menuItem);
2034 menuItem.addActionListener(actionListener);
2038 * Action on clicking sort annotations by type.
2042 protected void sortAnnotations_actionPerformed()
2047 * Action on clicking Show all annotations.
2049 * @param forSequences
2050 * update sequence-related annotations
2051 * @param forAlignment
2052 * update non-sequence-related annotations
2054 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2055 boolean forAlignment)
2057 setAnnotationsVisibility(true, forSequences, forAlignment);
2061 * Action on clicking Hide all annotations.
2063 * @param forSequences
2064 * update sequence-related annotations
2065 * @param forAlignment
2066 * update non-sequence-related annotations
2068 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2069 boolean forAlignment)
2071 setAnnotationsVisibility(false, forSequences, forAlignment);
2075 * Set the visibility of annotations to true or false. Can act on
2076 * sequence-related annotations, or alignment-related, or both.
2079 * @param forSequences
2080 * update sequence-related annotations
2081 * @param forAlignment
2082 * update non-sequence-related annotations
2084 protected void setAnnotationsVisibility(boolean visible,
2085 boolean forSequences, boolean forAlignment)
2090 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2092 // TODO Auto-generated method stub
2096 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2098 // TODO Auto-generated method stub
2102 protected void showAllhidden_actionPerformed(ActionEvent e)
2104 // TODO Auto-generated method stub
2108 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2110 // TODO Auto-generated method stub
2114 protected void hideAllSelection_actionPerformed(ActionEvent e)
2116 // TODO Auto-generated method stub
2120 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2122 // TODO Auto-generated method stub
2126 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2128 // TODO Auto-generated method stub
2132 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2134 // TODO Auto-generated method stub
2138 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2140 // TODO Auto-generated method stub
2144 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2146 // TODO Auto-generated method stub
2150 protected void showGroupConservation_actionPerformed(ActionEvent e)
2152 // TODO Auto-generated method stub
2156 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2158 // TODO Auto-generated method stub
2162 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2164 // TODO Auto-generated method stub
2168 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2170 // TODO Auto-generated method stub
2174 protected void followHighlight_actionPerformed()
2176 // TODO Auto-generated method stub
2180 protected void showNpFeats_actionPerformed(ActionEvent e)
2182 // TODO Auto-generated method stub
2186 protected void showDbRefs_actionPerformed(ActionEvent e)
2188 // TODO Auto-generated method stub
2192 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2196 protected void buildSortByAnnotationScoresMenu()
2200 protected void extractScores_actionPerformed(ActionEvent e)
2204 protected void outputText_actionPerformed(String formatName)
2208 public void addFromFile_actionPerformed(ActionEvent e)
2213 public void addFromText_actionPerformed(ActionEvent e)
2218 public void addFromURL_actionPerformed(ActionEvent e)
2223 public void exportFeatures_actionPerformed(ActionEvent e)
2228 public void exportAnnotations_actionPerformed(ActionEvent e)
2233 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2237 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2242 protected void closeMenuItem_actionPerformed(boolean b)
2246 protected void redoMenuItem_actionPerformed(ActionEvent e)
2250 protected void undoMenuItem_actionPerformed(ActionEvent e)
2254 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2258 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2262 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2266 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2270 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2274 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2278 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2282 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2286 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2290 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2294 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2298 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2302 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2306 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2310 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2314 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2318 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2322 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2326 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2330 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2334 protected void conservationMenuItem_actionPerformed(boolean selected)
2338 protected void printMenuItem_actionPerformed(ActionEvent e)
2342 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2346 protected void findMenuItem_actionPerformed(ActionEvent e)
2350 protected void abovePIDThreshold_actionPerformed(boolean selected)
2354 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2358 protected void deleteGroups_actionPerformed(ActionEvent e)
2362 protected void createGroup_actionPerformed(ActionEvent e)
2366 protected void unGroup_actionPerformed(ActionEvent e)
2370 protected void copy_actionPerformed(ActionEvent e)
2374 protected void cut_actionPerformed(ActionEvent e)
2378 protected void delete_actionPerformed(ActionEvent e)
2382 protected void pasteNew_actionPerformed(ActionEvent e)
2386 protected void pasteThis_actionPerformed(ActionEvent e)
2390 protected void applyToAllGroups_actionPerformed(boolean selected)
2394 public void createPNG(java.io.File f)
2398 protected void font_actionPerformed(ActionEvent e)
2402 protected void seqLimit_actionPerformed(ActionEvent e)
2406 public void seqDBRef_actionPerformed(ActionEvent e)
2411 public void createEPS(java.io.File f)
2415 public void createSVG(java.io.File f)
2420 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2426 * Template method to handle the 'load T-Coffee scores' menu event.
2428 * Subclasses override this method to provide a custom action.
2433 protected void loadScores_actionPerformed(ActionEvent event)
2438 protected void jpred_actionPerformed(ActionEvent e)
2442 protected void scaleAbove_actionPerformed(ActionEvent e)
2446 protected void scaleLeft_actionPerformed(ActionEvent e)
2450 protected void scaleRight_actionPerformed(ActionEvent e)
2454 protected void modifyPID_actionPerformed()
2458 protected void modifyConservation_actionPerformed()
2462 protected void saveAs_actionPerformed()
2466 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2470 public void vamsasStore_actionPerformed(ActionEvent e)
2475 public void vamsasLoad_actionPerformed(ActionEvent e)
2480 public void showTranslation_actionPerformed(ActionEvent e)
2485 public void featureSettings_actionPerformed(ActionEvent e)
2490 public void fetchSequence_actionPerformed(ActionEvent e)
2495 public void smoothFont_actionPerformed(ActionEvent e)
2500 public void annotationColour_actionPerformed()
2504 public void annotationColumn_actionPerformed(ActionEvent e)
2508 public void associatedData_actionPerformed(ActionEvent e)
2513 public void autoCalculate_actionPerformed(ActionEvent e)
2518 public void sortByTreeOption_actionPerformed(ActionEvent e)
2523 public void showAllSeqs_actionPerformed(ActionEvent e)
2528 public void showAllColumns_actionPerformed(ActionEvent e)
2533 public void hideSelSequences_actionPerformed(ActionEvent e)
2538 public void hideSelColumns_actionPerformed(ActionEvent e)
2543 public void hiddenMarkers_actionPerformed(ActionEvent e)
2548 public void findPdbId_actionPerformed(ActionEvent e)
2553 public void enterPdbId_actionPerformed(ActionEvent e)
2558 public void pdbFile_actionPerformed(ActionEvent e)
2563 public void invertColSel_actionPerformed(ActionEvent e)
2568 public void tabSelectionChanged(int sel)
2573 public void tabbedPane_mousePressed(MouseEvent e)
2578 public void tabbedPane_focusGained(FocusEvent e)
2583 public void save_actionPerformed(ActionEvent e)
2588 public void reload_actionPerformed(ActionEvent e)
2593 public void newView_actionPerformed(ActionEvent e)
2598 public void textColour_actionPerformed()
2603 public void idRightAlign_actionPerformed(ActionEvent e)
2608 public void expandViews_actionPerformed(ActionEvent e)
2613 public void gatherViews_actionPerformed(ActionEvent e)
2618 public void buildTreeSortMenu()
2623 public void pageSetup_actionPerformed(ActionEvent e)
2628 public void alignmentProperties()
2633 protected void expand_newalign(ActionEvent e)
2635 // TODO Auto-generated method stub
2639 protected boolean isShowAutoCalculatedAbove()
2641 return showAutoCalculatedAbove;
2644 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2646 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2649 protected SequenceAnnotationOrder getAnnotationSortOrder()
2651 return annotationSortOrder;
2654 protected void setAnnotationSortOrder(
2655 SequenceAnnotationOrder annotationSortOrder)
2657 this.annotationSortOrder = annotationSortOrder;
2660 public Map<KeyStroke, JMenuItem> getAccelerators()
2662 return this.accelerators;
2666 * Returns the selected index of the tabbed pane, or -1 if none selected
2667 * (including the case where the tabbed pane has not been made visible).
2671 public int getTabIndex()
2673 return tabbedPane.getSelectedIndex();
2676 public JPanel getStatusPanel()
2682 * Sets a reference to the containing split frame. Also makes the 'toggle
2683 * split view' menu item visible and checked.
2687 public void setSplitFrame(SplitContainerI sf)
2689 this.splitFrame = sf;
2692 this.showComplementMenuItem.setVisible(true);
2693 this.showComplementMenuItem.setState(true);
2697 public SplitContainerI getSplitViewContainer()
2699 return this.splitFrame;
2702 protected void showComplement_actionPerformed(boolean complement)