2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.analysis.GeneticCodeI;
25 import jalview.analysis.GeneticCodes;
26 import jalview.api.SplitContainerI;
27 import jalview.bin.Cache;
28 import jalview.gui.JvSwingUtils;
29 import jalview.gui.PaintRefresher;
30 import jalview.gui.Preferences;
31 import jalview.gui.TreePanel;
32 import jalview.io.FileFormats;
33 import jalview.schemes.ResidueColourScheme;
34 import jalview.util.MessageManager;
35 import jalview.util.Platform;
37 import java.awt.BorderLayout;
38 import java.awt.Color;
39 import java.awt.Component;
40 import java.awt.GridLayout;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.FocusAdapter;
44 import java.awt.event.FocusEvent;
45 import java.awt.event.KeyEvent;
46 import java.awt.event.MouseAdapter;
47 import java.awt.event.MouseEvent;
48 import java.util.ArrayList;
49 import java.util.HashMap;
50 import java.util.List;
53 import javax.swing.BorderFactory;
54 import javax.swing.ButtonGroup;
55 import javax.swing.JCheckBoxMenuItem;
56 import javax.swing.JInternalFrame;
57 import javax.swing.JLabel;
58 import javax.swing.JMenu;
59 import javax.swing.JMenuBar;
60 import javax.swing.JMenuItem;
61 import javax.swing.JPanel;
62 import javax.swing.JRadioButtonMenuItem;
63 import javax.swing.JTabbedPane;
64 import javax.swing.KeyStroke;
65 import javax.swing.event.ChangeEvent;
66 import javax.swing.event.MenuEvent;
67 import javax.swing.event.MenuListener;
69 @SuppressWarnings("serial")
70 public class GAlignFrame extends JInternalFrame
72 protected JMenuBar alignFrameMenuBar = new JMenuBar();
74 protected JMenuItem closeMenuItem = new JMenuItem();
76 public JMenu webService = new JMenu();// BH 2019 was protected, but not
77 // sufficient for AlignFrame thread run
79 public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
80 // sufficient for AlignFrame thread run
82 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
84 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
86 protected JMenu sortByAnnotScore = new JMenu();
88 public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
90 // AlignFrame.printWriter
92 protected JMenu outputTextboxMenu = new JMenu();
94 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
96 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
98 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
100 protected JMenuItem undoMenuItem = new JMenuItem();
102 protected JMenuItem redoMenuItem = new JMenuItem();
104 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
106 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
108 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
110 JMenuItem copy = new JMenuItem();
112 JMenuItem cut = new JMenuItem();
114 JMenu pasteMenu = new JMenu();
116 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
118 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
120 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
122 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
124 protected JCheckBoxMenuItem applyToAllGroups;
126 protected JMenu colourMenu = new JMenu();
128 protected JMenuItem textColour;
130 protected JCheckBoxMenuItem conservationMenuItem;
132 protected JMenuItem modifyConservation;
134 protected JCheckBoxMenuItem abovePIDThreshold;
136 protected JMenuItem modifyPID;
138 protected JRadioButtonMenuItem annotationColour;
140 protected JMenu sortByTreeMenu = new JMenu();
142 protected JMenu sort = new JMenu();
144 protected JMenuItem calculateTree = new JMenuItem();
146 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
148 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
150 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
152 protected JMenu showTranslation = new JMenu();
154 protected JMenuItem showReverse = new JMenuItem();
156 protected JMenuItem showReverseComplement = new JMenuItem();
158 protected JMenu showProducts = new JMenu();
160 protected JMenuItem runGroovy = new JMenuItem();
162 protected JMenuItem loadVcf;
164 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
166 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
168 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
170 protected JPanel statusPanel = new JPanel();
172 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
174 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
176 protected JMenuItem showAllAlAnnotations = new JMenuItem();
178 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
180 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
182 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
184 protected JTabbedPane tabbedPane = new JTabbedPane();
186 protected JMenuItem reload = new JMenuItem();
188 protected JMenu formatMenu = new JMenu();
190 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
192 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
194 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
196 protected JMenuItem gatherViews = new JMenuItem();
198 protected JMenuItem expandViews = new JMenuItem();
200 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
202 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
204 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
206 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
208 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
210 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
212 protected JMenuItem openFeatureSettings;
214 private SequenceAnnotationOrder annotationSortOrder;
216 private boolean showAutoCalculatedAbove = false;
218 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
220 private SplitContainerI splitFrame;
227 // for Web-page embedding using id=align-frame-div
228 setName(Platform.getAppID("alignment"));
232 setJMenuBar(alignFrameMenuBar);
234 // dynamically fill save as menu with available formats
235 for (String ff : FileFormats.getInstance().getWritableFormats(true))
237 JMenuItem item = new JMenuItem(ff);
239 item.addActionListener(new ActionListener()
242 public void actionPerformed(ActionEvent e)
244 outputText_actionPerformed(e.getActionCommand());
248 outputTextboxMenu.add(item);
250 } catch (Exception e)
252 System.err.println(e.toString());
255 if (Platform.allowMnemonics()) // was "not mac and not JS"
257 closeMenuItem.setMnemonic('C');
258 outputTextboxMenu.setMnemonic('T');
259 undoMenuItem.setMnemonic('Z');
260 redoMenuItem.setMnemonic('0');
261 copy.setMnemonic('C');
262 cut.setMnemonic('U');
263 pasteMenu.setMnemonic('P');
264 reload.setMnemonic('R');
268 private void jbInit() throws Exception
272 JMenuItem saveAs = new JMenuItem(
273 MessageManager.getString("action.save_as"));
274 ActionListener al = new ActionListener()
277 public void actionPerformed(ActionEvent e)
279 saveAs_actionPerformed();
283 // FIXME getDefaultToolkit throws an exception in Headless mode
284 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
285 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
286 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
288 addMenuActionAndAccelerator(keyStroke, saveAs, al);
290 closeMenuItem.setText(MessageManager.getString("action.close"));
291 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
292 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
293 al = new ActionListener()
296 public void actionPerformed(ActionEvent e)
298 closeMenuItem_actionPerformed(false);
301 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
303 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
304 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
305 JMenu annotationsMenu = new JMenu(
306 MessageManager.getString("action.annotations"));
307 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
308 colourMenu.setText(MessageManager.getString("action.colour"));
309 JMenu calculateMenu = new JMenu(
310 MessageManager.getString("action.calculate"));
311 webService.setText(MessageManager.getString("action.web_service"));
312 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
313 MessageManager.getString("action.select_all"));
314 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
315 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
316 al = new ActionListener()
319 public void actionPerformed(ActionEvent e)
321 selectAllSequenceMenuItem_actionPerformed(e);
324 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
326 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
327 MessageManager.getString("action.deselect_all"));
328 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
329 al = new ActionListener()
332 public void actionPerformed(ActionEvent e)
334 deselectAllSequenceMenuItem_actionPerformed(e);
337 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
339 JMenuItem invertSequenceMenuItem = new JMenuItem(
340 MessageManager.getString("action.invert_sequence_selection"));
341 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
342 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
343 al = new ActionListener()
346 public void actionPerformed(ActionEvent e)
348 invertSequenceMenuItem_actionPerformed(e);
351 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
353 JMenuItem grpsFromSelection = new JMenuItem(
354 MessageManager.getString("action.make_groups_selection"));
355 grpsFromSelection.addActionListener(new ActionListener()
358 public void actionPerformed(ActionEvent e)
360 makeGrpsFromSelection_actionPerformed(e);
363 JMenuItem expandAlignment = new JMenuItem(
364 MessageManager.getString("action.view_flanking_regions"));
365 expandAlignment.setToolTipText(
366 MessageManager.getString("label.view_flanking_regions"));
367 expandAlignment.addActionListener(new ActionListener()
370 public void actionPerformed(ActionEvent e)
375 JMenuItem remove2LeftMenuItem = new JMenuItem(
376 MessageManager.getString("action.remove_left"));
377 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
378 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
379 al = new ActionListener()
382 public void actionPerformed(ActionEvent e)
384 remove2LeftMenuItem_actionPerformed(e);
387 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
389 JMenuItem remove2RightMenuItem = new JMenuItem(
390 MessageManager.getString("action.remove_right"));
391 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
392 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
393 al = new ActionListener()
396 public void actionPerformed(ActionEvent e)
398 remove2RightMenuItem_actionPerformed(e);
401 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
403 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
404 MessageManager.getString("action.remove_empty_columns"));
405 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
406 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
407 al = new ActionListener()
410 public void actionPerformed(ActionEvent e)
412 removeGappedColumnMenuItem_actionPerformed(e);
415 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
417 JMenuItem removeAllGapsMenuItem = new JMenuItem(
418 MessageManager.getString("action.remove_all_gaps"));
419 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
420 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
421 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
423 al = new ActionListener()
426 public void actionPerformed(ActionEvent e)
428 removeAllGapsMenuItem_actionPerformed(e);
431 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
433 JMenuItem justifyLeftMenuItem = new JMenuItem(
434 MessageManager.getString("action.left_justify_alignment"));
435 justifyLeftMenuItem.addActionListener(new ActionListener()
438 public void actionPerformed(ActionEvent e)
440 justifyLeftMenuItem_actionPerformed(e);
443 JMenuItem justifyRightMenuItem = new JMenuItem(
444 MessageManager.getString("action.right_justify_alignment"));
445 justifyRightMenuItem.addActionListener(new ActionListener()
448 public void actionPerformed(ActionEvent e)
450 justifyRightMenuItem_actionPerformed(e);
453 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
454 viewBoxesMenuItem.setState(true);
455 viewBoxesMenuItem.addActionListener(new ActionListener()
458 public void actionPerformed(ActionEvent e)
460 viewBoxesMenuItem_actionPerformed(e);
463 viewTextMenuItem.setText(MessageManager.getString("action.text"));
464 viewTextMenuItem.setState(true);
465 viewTextMenuItem.addActionListener(new ActionListener()
468 public void actionPerformed(ActionEvent e)
470 viewTextMenuItem_actionPerformed(e);
473 showNonconservedMenuItem
474 .setText(MessageManager.getString("label.show_non_conserved"));
475 showNonconservedMenuItem.setState(false);
476 showNonconservedMenuItem.addActionListener(new ActionListener()
479 public void actionPerformed(ActionEvent e)
481 showUnconservedMenuItem_actionPerformed(e);
484 JMenuItem sortPairwiseMenuItem = new JMenuItem(
485 MessageManager.getString("action.by_pairwise_id"));
486 sortPairwiseMenuItem.addActionListener(new ActionListener()
489 public void actionPerformed(ActionEvent e)
491 sortPairwiseMenuItem_actionPerformed(e);
494 JMenuItem sortIDMenuItem = new JMenuItem(
495 MessageManager.getString("action.by_id"));
496 sortIDMenuItem.addActionListener(new ActionListener()
499 public void actionPerformed(ActionEvent e)
501 sortIDMenuItem_actionPerformed(e);
504 JMenuItem sortLengthMenuItem = new JMenuItem(
505 MessageManager.getString("action.by_length"));
506 sortLengthMenuItem.addActionListener(new ActionListener()
509 public void actionPerformed(ActionEvent e)
511 sortLengthMenuItem_actionPerformed(e);
514 JMenuItem sortGroupMenuItem = new JMenuItem(
515 MessageManager.getString("action.by_group"));
516 sortGroupMenuItem.addActionListener(new ActionListener()
519 public void actionPerformed(ActionEvent e)
521 sortGroupMenuItem_actionPerformed(e);
525 JMenuItem removeRedundancyMenuItem = new JMenuItem(
526 MessageManager.getString("action.remove_redundancy"));
527 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
528 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
529 al = new ActionListener()
532 public void actionPerformed(ActionEvent e)
534 removeRedundancyMenuItem_actionPerformed(e);
537 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
539 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
540 MessageManager.getString("action.pairwise_alignment"));
541 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
544 public void actionPerformed(ActionEvent e)
546 pairwiseAlignmentMenuItem_actionPerformed(e);
550 this.getContentPane().setLayout(new BorderLayout());
551 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
552 statusBar.setBackground(Color.white);
553 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
554 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
555 statusBar.setText(MessageManager.getString("label.status_bar"));
557 .setText(MessageManager.getString("label.out_to_textbox"));
559 annotationPanelMenuItem.setActionCommand("");
560 annotationPanelMenuItem
561 .setText(MessageManager.getString("label.show_annotations"));
562 annotationPanelMenuItem
563 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
564 annotationPanelMenuItem.addActionListener(new ActionListener()
567 public void actionPerformed(ActionEvent e)
569 annotationPanelMenuItem_actionPerformed(e);
572 showAllAlAnnotations.setText(
573 MessageManager.getString("label.show_all_al_annotations"));
574 final boolean isAnnotationPanelShown = annotationPanelMenuItem
576 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
577 showAllAlAnnotations.addActionListener(new ActionListener()
580 public void actionPerformed(ActionEvent e)
582 showAllAnnotations_actionPerformed(false, true);
585 hideAllAlAnnotations.setText(
586 MessageManager.getString("label.hide_all_al_annotations"));
587 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
588 hideAllAlAnnotations.addActionListener(new ActionListener()
591 public void actionPerformed(ActionEvent e)
593 hideAllAnnotations_actionPerformed(false, true);
596 showAllSeqAnnotations.setText(
597 MessageManager.getString("label.show_all_seq_annotations"));
598 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
599 showAllSeqAnnotations.addActionListener(new ActionListener()
602 public void actionPerformed(ActionEvent e)
604 showAllAnnotations_actionPerformed(true, false);
607 hideAllSeqAnnotations.setText(
608 MessageManager.getString("label.hide_all_seq_annotations"));
609 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
610 hideAllSeqAnnotations.addActionListener(new ActionListener()
613 public void actionPerformed(ActionEvent e)
615 hideAllAnnotations_actionPerformed(true, false);
618 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
619 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
620 SequenceAnnotationOrder.NONE.name()));
621 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
622 MessageManager.getString("label.sort_annotations_by_sequence"));
623 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
624 MessageManager.getString("label.sort_annotations_by_label"));
626 sortAnnBySequence.setSelected(
627 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
628 sortAnnBySequence.addActionListener(new ActionListener()
631 public void actionPerformed(ActionEvent e)
633 boolean newState = sortAnnBySequence.getState();
634 sortAnnByLabel.setSelected(false);
635 setAnnotationSortOrder(
636 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
637 : SequenceAnnotationOrder.NONE);
638 sortAnnotations_actionPerformed();
641 sortAnnByLabel.setSelected(
642 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
643 sortAnnByLabel.addActionListener(new ActionListener()
646 public void actionPerformed(ActionEvent e)
648 boolean newState = sortAnnByLabel.getState();
649 sortAnnBySequence.setSelected(false);
650 setAnnotationSortOrder(
651 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
652 : SequenceAnnotationOrder.NONE);
653 sortAnnotations_actionPerformed();
656 colourTextMenuItem = new JCheckBoxMenuItem(
657 MessageManager.getString("label.colour_text"));
658 colourTextMenuItem.addActionListener(new ActionListener()
661 public void actionPerformed(ActionEvent e)
663 colourTextMenuItem_actionPerformed(e);
667 JMenuItem htmlMenuItem = new JMenuItem(
668 MessageManager.getString("label.html"));
669 htmlMenuItem.addActionListener(new ActionListener()
672 public void actionPerformed(ActionEvent e)
674 htmlMenuItem_actionPerformed(e);
678 JMenuItem createBioJS = new JMenuItem(
679 MessageManager.getString("label.biojs_html_export"));
680 createBioJS.addActionListener(new java.awt.event.ActionListener()
683 public void actionPerformed(ActionEvent e)
685 bioJSMenuItem_actionPerformed(e);
689 JMenuItem overviewMenuItem = new JMenuItem(
690 MessageManager.getString("label.overview_window"));
691 overviewMenuItem.addActionListener(new ActionListener()
694 public void actionPerformed(ActionEvent e)
696 overviewMenuItem_actionPerformed(e);
700 undoMenuItem.setEnabled(false);
701 undoMenuItem.setText(MessageManager.getString("action.undo"));
702 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
703 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
704 al = new ActionListener()
707 public void actionPerformed(ActionEvent e)
709 undoMenuItem_actionPerformed(e);
712 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
714 redoMenuItem.setEnabled(false);
715 redoMenuItem.setText(MessageManager.getString("action.redo"));
716 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
717 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
718 al = new ActionListener()
721 public void actionPerformed(ActionEvent e)
723 redoMenuItem_actionPerformed(e);
726 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
728 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
729 wrapMenuItem.addActionListener(new ActionListener()
732 public void actionPerformed(ActionEvent e)
734 wrapMenuItem_actionPerformed(e);
738 JMenuItem printMenuItem = new JMenuItem(
739 MessageManager.getString("action.print"));
740 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
741 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
742 al = new ActionListener()
745 public void actionPerformed(ActionEvent e)
747 printMenuItem_actionPerformed(e);
750 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
753 .setText(MessageManager.getString("action.show_gaps"));
754 renderGapsMenuItem.setState(true);
755 renderGapsMenuItem.addActionListener(new ActionListener()
758 public void actionPerformed(ActionEvent e)
760 renderGapsMenuItem_actionPerformed(e);
764 JMenuItem findMenuItem = new JMenuItem(
765 MessageManager.getString("action.find"));
766 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
767 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
768 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
769 MessageManager.getString("label.find_tip")));
770 al = new ActionListener()
773 public void actionPerformed(ActionEvent e)
775 findMenuItem_actionPerformed(e);
778 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
780 showSeqFeatures.setText(
781 MessageManager.getString("label.show_sequence_features"));
782 showSeqFeatures.addActionListener(new ActionListener()
785 public void actionPerformed(ActionEvent actionEvent)
787 showSeqFeatures_actionPerformed(actionEvent);
791 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
792 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
793 * void actionPerformed(ActionEvent actionEvent) {
794 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
797 .setText(MessageManager.getString("label.show_database_refs"));
798 showDbRefsMenuitem.addActionListener(new ActionListener()
802 public void actionPerformed(ActionEvent e)
804 showDbRefs_actionPerformed(e);
808 showNpFeatsMenuitem.setText(
809 MessageManager.getString("label.show_non_positional_features"));
810 showNpFeatsMenuitem.addActionListener(new ActionListener()
814 public void actionPerformed(ActionEvent e)
816 showNpFeats_actionPerformed(e);
820 showGroupConservation
821 .setText(MessageManager.getString("label.group_conservation"));
822 showGroupConservation.addActionListener(new ActionListener()
826 public void actionPerformed(ActionEvent e)
828 showGroupConservation_actionPerformed(e);
834 .setText(MessageManager.getString("label.group_consensus"));
835 showGroupConsensus.addActionListener(new ActionListener()
839 public void actionPerformed(ActionEvent e)
841 showGroupConsensus_actionPerformed(e);
845 showConsensusHistogram.setText(
846 MessageManager.getString("label.show_consensus_histogram"));
847 showConsensusHistogram.addActionListener(new ActionListener()
851 public void actionPerformed(ActionEvent e)
853 showConsensusHistogram_actionPerformed(e);
858 .setText(MessageManager.getString("label.show_consensus_logo"));
859 showSequenceLogo.addActionListener(new ActionListener()
863 public void actionPerformed(ActionEvent e)
865 showSequenceLogo_actionPerformed(e);
869 normaliseSequenceLogo
870 .setText(MessageManager.getString("label.norm_consensus_logo"));
871 normaliseSequenceLogo.addActionListener(new ActionListener()
875 public void actionPerformed(ActionEvent e)
877 normaliseSequenceLogo_actionPerformed(e);
881 applyAutoAnnotationSettings
882 .setText(MessageManager.getString("label.apply_all_groups"));
883 applyAutoAnnotationSettings.setState(false);
884 applyAutoAnnotationSettings.setVisible(true);
885 applyAutoAnnotationSettings.addActionListener(new ActionListener()
888 public void actionPerformed(ActionEvent e)
890 applyAutoAnnotationSettings_actionPerformed(e);
894 ButtonGroup buttonGroup = new ButtonGroup();
895 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
896 MessageManager.getString("label.show_first"));
897 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
898 MessageManager.getString("label.show_last"));
899 buttonGroup.add(showAutoFirst);
900 buttonGroup.add(showAutoLast);
901 final boolean autoFirst = Cache
902 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
903 showAutoFirst.setSelected(autoFirst);
904 setShowAutoCalculatedAbove(autoFirst);
905 showAutoFirst.addActionListener(new ActionListener()
908 public void actionPerformed(ActionEvent e)
910 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
911 sortAnnotations_actionPerformed();
914 showAutoLast.setSelected(!showAutoFirst.isSelected());
915 showAutoLast.addActionListener(new ActionListener()
918 public void actionPerformed(ActionEvent e)
920 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
921 sortAnnotations_actionPerformed();
925 JMenuItem deleteGroups = new JMenuItem(
926 MessageManager.getString("action.undefine_groups"));
927 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
928 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
929 al = new ActionListener()
932 public void actionPerformed(ActionEvent e)
934 deleteGroups_actionPerformed(e);
937 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
939 JMenuItem annotationColumn = new JMenuItem(
940 MessageManager.getString("action.select_by_annotation"));
941 annotationColumn.addActionListener(new ActionListener()
944 public void actionPerformed(ActionEvent e)
946 annotationColumn_actionPerformed(e);
950 JMenuItem createGroup = new JMenuItem(
951 MessageManager.getString("action.create_group"));
952 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
953 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
954 al = new ActionListener()
957 public void actionPerformed(ActionEvent e)
959 createGroup_actionPerformed(e);
962 addMenuActionAndAccelerator(keyStroke, createGroup, al);
964 JMenuItem unGroup = new JMenuItem(
965 MessageManager.getString("action.remove_group"));
966 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
967 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
968 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
970 al = new ActionListener()
973 public void actionPerformed(ActionEvent e)
975 unGroup_actionPerformed(e);
978 addMenuActionAndAccelerator(keyStroke, unGroup, al);
980 copy.setText(MessageManager.getString("action.copy"));
981 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
982 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
984 al = new ActionListener()
987 public void actionPerformed(ActionEvent e)
989 copy_actionPerformed();
992 addMenuActionAndAccelerator(keyStroke, copy, al);
994 cut.setText(MessageManager.getString("action.cut"));
995 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
996 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
997 al = new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 cut_actionPerformed();
1005 addMenuActionAndAccelerator(keyStroke, cut, al);
1007 JMenuItem delete = new JMenuItem(
1008 MessageManager.getString("action.delete"));
1009 delete.addActionListener(new ActionListener()
1012 public void actionPerformed(ActionEvent e)
1014 delete_actionPerformed();
1018 pasteMenu.setText(MessageManager.getString("action.paste"));
1019 JMenuItem pasteNew = new JMenuItem(
1020 MessageManager.getString("label.to_new_alignment"));
1021 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1022 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1023 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1025 al = new ActionListener()
1028 public void actionPerformed(ActionEvent e)
1030 pasteNew_actionPerformed(e);
1033 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1035 JMenuItem pasteThis = new JMenuItem(
1036 MessageManager.getString("label.to_this_alignment"));
1037 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1038 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1039 al = new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 pasteThis_actionPerformed(e);
1047 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1049 JMenuItem createPNG = new JMenuItem("PNG");
1050 createPNG.addActionListener(new ActionListener()
1053 public void actionPerformed(ActionEvent e)
1058 createPNG.setActionCommand(
1059 MessageManager.getString("label.save_png_image"));
1061 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1062 font.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 font_actionPerformed(e);
1071 MessageManager.getString("label.show_sequence_limits"));
1072 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1073 seqLimits.addActionListener(new ActionListener()
1076 public void actionPerformed(ActionEvent e)
1078 seqLimit_actionPerformed(e);
1081 JMenuItem epsFile = new JMenuItem("EPS");
1082 epsFile.addActionListener(new ActionListener()
1085 public void actionPerformed(ActionEvent e)
1091 JMenuItem createSVG = new JMenuItem("SVG");
1092 createSVG.addActionListener(new ActionListener()
1095 public void actionPerformed(ActionEvent e)
1101 JMenuItem loadTreeMenuItem = new JMenuItem(
1102 MessageManager.getString("label.load_associated_tree"));
1103 loadTreeMenuItem.setActionCommand(
1104 MessageManager.getString("label.load_tree_for_sequence_set"));
1105 loadTreeMenuItem.addActionListener(new ActionListener()
1108 public void actionPerformed(ActionEvent e)
1110 loadTreeMenuItem_actionPerformed(e);
1114 scaleAbove.setVisible(false);
1115 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1116 scaleAbove.addActionListener(new ActionListener()
1119 public void actionPerformed(ActionEvent e)
1121 scaleAbove_actionPerformed(e);
1124 scaleLeft.setVisible(false);
1125 scaleLeft.setSelected(true);
1126 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1127 scaleLeft.addActionListener(new ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 scaleLeft_actionPerformed(e);
1135 scaleRight.setVisible(false);
1136 scaleRight.setSelected(true);
1137 scaleRight.setText(MessageManager.getString("action.scale_right"));
1138 scaleRight.addActionListener(new ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 scaleRight_actionPerformed(e);
1146 centreColumnLabelsMenuItem.setVisible(true);
1147 centreColumnLabelsMenuItem.setState(false);
1148 centreColumnLabelsMenuItem.setText(
1149 MessageManager.getString("label.centre_column_labels"));
1150 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1153 public void actionPerformed(ActionEvent e)
1155 centreColumnLabels_actionPerformed(e);
1158 followHighlightMenuItem.setVisible(true);
1159 followHighlightMenuItem.setState(true);
1160 followHighlightMenuItem
1161 .setText(MessageManager.getString("label.automatic_scrolling"));
1162 followHighlightMenuItem.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 followHighlight_actionPerformed();
1174 .setText(MessageManager.getString("action.by_tree_order"));
1175 sort.setText(MessageManager.getString("action.sort"));
1176 sort.addMenuListener(new MenuListener()
1179 public void menuSelected(MenuEvent e)
1181 enableSortMenuOptions();
1185 public void menuDeselected(MenuEvent e)
1190 public void menuCanceled(MenuEvent e)
1194 sortByTreeMenu.addMenuListener(new MenuListener()
1197 public void menuSelected(MenuEvent e)
1199 buildTreeSortMenu();
1203 public void menuDeselected(MenuEvent e)
1208 public void menuCanceled(MenuEvent e)
1213 .setText(MessageManager.getString("label.sort_by_score"));
1214 sort.add(sortByAnnotScore);
1215 sort.addMenuListener(new javax.swing.event.MenuListener()
1219 public void menuCanceled(MenuEvent e)
1224 public void menuDeselected(MenuEvent e)
1229 public void menuSelected(MenuEvent e)
1231 buildSortByAnnotationScoresMenu();
1234 sortByAnnotScore.setVisible(false);
1237 .setText(MessageManager.getString("action.calculate_tree_pca"));
1239 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1241 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1242 padGapsMenuitem.addActionListener(new ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 padGapsMenuitem_actionPerformed(e);
1250 JMenuItem vamsasStore = new JMenuItem(
1251 MessageManager.getString("label.vamsas_store"));
1252 vamsasStore.setVisible(false);
1253 vamsasStore.addActionListener(new ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 vamsasStore_actionPerformed(e);
1263 * Translate as cDNA with sub-menu of translation tables
1266 .setText(MessageManager.getString("label.translate_cDNA"));
1267 boolean first = true;
1268 for (final GeneticCodeI table : GeneticCodes.getInstance()
1271 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1272 showTranslation.add(item);
1273 item.addActionListener(new ActionListener()
1276 public void actionPerformed(ActionEvent e)
1278 showTranslation_actionPerformed(table);
1283 showTranslation.addSeparator();
1288 showReverse.setText(MessageManager.getString("label.reverse"));
1289 showReverse.addActionListener(new ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 showReverse_actionPerformed(false);
1297 showReverseComplement
1298 .setText(MessageManager.getString("label.reverse_complement"));
1299 showReverseComplement.addActionListener(new ActionListener()
1302 public void actionPerformed(ActionEvent e)
1304 showReverse_actionPerformed(true);
1308 JMenuItem extractScores = new JMenuItem(
1309 MessageManager.getString("label.extract_scores"));
1310 extractScores.addActionListener(new ActionListener()
1313 public void actionPerformed(ActionEvent e)
1315 extractScores_actionPerformed(e);
1318 extractScores.setVisible(true);
1319 // JBPNote: TODO: make gui for regex based score extraction
1321 // for show products actions see AlignFrame.canShowProducts
1322 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1324 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1325 runGroovy.setToolTipText(
1326 MessageManager.getString("label.run_groovy_tip"));
1327 runGroovy.addActionListener(new ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 runGroovy_actionPerformed();
1336 openFeatureSettings = new JMenuItem(
1337 MessageManager.getString("action.feature_settings"));
1338 openFeatureSettings.addActionListener(new ActionListener()
1341 public void actionPerformed(ActionEvent e)
1343 featureSettings_actionPerformed(e);
1348 * add sub-menu of database we can fetch from
1350 JMenuItem fetchSequence = new JMenuItem(
1351 MessageManager.getString("label.fetch_sequences"));
1352 fetchSequence.addActionListener(new ActionListener()
1355 public void actionPerformed(ActionEvent e)
1357 fetchSequence_actionPerformed();
1361 JMenuItem associatedData = new JMenuItem(
1362 MessageManager.getString("label.load_features_annotations"));
1363 associatedData.addActionListener(new ActionListener()
1366 public void actionPerformed(ActionEvent e)
1368 associatedData_actionPerformed(e);
1371 loadVcf = new JMenuItem(
1372 MessageManager.getString("label.load_vcf_file"));
1373 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1374 loadVcf.addActionListener(new ActionListener()
1377 public void actionPerformed(ActionEvent e)
1379 loadVcf_actionPerformed();
1382 autoCalculate.setText(
1383 MessageManager.getString("label.autocalculate_consensus"));
1384 autoCalculate.setState(
1385 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1386 autoCalculate.addActionListener(new ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 autoCalculate_actionPerformed(e);
1395 MessageManager.getString("label.sort_alignment_new_tree"));
1396 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1397 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1399 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1400 sortByTree.addActionListener(new ActionListener()
1403 public void actionPerformed(ActionEvent e)
1405 sortByTreeOption_actionPerformed(e);
1409 listenToViewSelections.setText(
1410 MessageManager.getString("label.listen_for_selections"));
1411 listenToViewSelections
1412 .setToolTipText("<html>" + MessageManager.getString(
1413 "label.selections_mirror_selections_made_same_sequences_other_views"));
1414 listenToViewSelections.setState(false);
1415 listenToViewSelections.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 listenToViewSelections_actionPerformed(e);
1424 JMenu addSequenceMenu = new JMenu(
1425 MessageManager.getString("label.add_sequences"));
1426 JMenuItem addFromFile = new JMenuItem(
1427 MessageManager.getString("label.from_file"));
1428 addFromFile.addActionListener(new ActionListener()
1431 public void actionPerformed(ActionEvent e)
1433 addFromFile_actionPerformed(e);
1436 JMenuItem addFromText = new JMenuItem(
1437 MessageManager.getString("label.from_textbox"));
1438 addFromText.addActionListener(new ActionListener()
1441 public void actionPerformed(ActionEvent e)
1443 addFromText_actionPerformed(e);
1446 JMenuItem addFromURL = new JMenuItem(
1447 MessageManager.getString("label.from_url"));
1448 addFromURL.addActionListener(new ActionListener()
1451 public void actionPerformed(ActionEvent e)
1453 addFromURL_actionPerformed(e);
1456 JMenuItem exportFeatures = new JMenuItem(
1457 MessageManager.getString("label.export_features"));
1458 exportFeatures.addActionListener(new ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 exportFeatures_actionPerformed(e);
1466 JMenuItem exportAnnotations = new JMenuItem(
1467 MessageManager.getString("label.export_annotations"));
1468 exportAnnotations.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent e)
1473 exportAnnotations_actionPerformed(e);
1476 statusPanel.setLayout(new GridLayout());
1477 JMenuItem showAllSeqs = new JMenuItem(
1478 MessageManager.getString("label.all_sequences"));
1479 showAllSeqs.setToolTipText(
1480 MessageManager.getString("label.toggle_sequence_visibility"));
1481 showAllSeqs.addActionListener(new ActionListener()
1484 public void actionPerformed(ActionEvent e)
1486 showAllSeqs_actionPerformed(e);
1489 JMenuItem showAllColumns = new JMenuItem(
1490 MessageManager.getString("label.all_columns"));
1491 showAllColumns.setToolTipText(
1492 MessageManager.getString("label.toggle_columns_visibility"));
1493 showAllColumns.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 showAllColumns_actionPerformed(e);
1501 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1502 JMenuItem hideSelSequences = new JMenuItem(
1503 MessageManager.getString("label.selected_sequences"));
1504 hideSelSequences.setToolTipText(
1505 MessageManager.getString("label.toggle_sequence_visibility"));
1506 hideSelSequences.addActionListener(new ActionListener()
1509 public void actionPerformed(ActionEvent e)
1511 hideSelSequences_actionPerformed(e);
1514 JMenuItem hideSelColumns = new JMenuItem(
1515 MessageManager.getString("label.selected_columns"));
1516 hideSelColumns.setToolTipText(
1517 MessageManager.getString("label.toggle_columns_visibility"));
1518 hideSelColumns.addActionListener(new ActionListener()
1521 public void actionPerformed(ActionEvent e)
1523 hideSelColumns_actionPerformed(e);
1526 JMenuItem hideAllSelection = new JMenuItem(
1527 MessageManager.getString("label.selected_region"));
1528 hideAllSelection.addActionListener(new ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 hideAllSelection_actionPerformed(e);
1536 // TODO: should be hidden if no selection exists.
1537 JMenuItem hideAllButSelection = new JMenuItem(
1538 MessageManager.getString("label.all_but_selected_region"));
1539 hideAllButSelection.addActionListener(new ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 hideAllButSelection_actionPerformed(e);
1547 JMenuItem showAllhidden = new JMenuItem(
1548 MessageManager.getString("label.all_sequences_columns"));
1549 showAllhidden.setToolTipText(MessageManager
1550 .getString("label.toggles_visibility_hidden_selected_regions"));
1551 showAllhidden.addActionListener(new ActionListener()
1554 public void actionPerformed(ActionEvent e)
1556 showAllhidden_actionPerformed(e);
1559 hiddenMarkers.setText(
1560 MessageManager.getString("action.show_hidden_markers"));
1561 hiddenMarkers.addActionListener(new ActionListener()
1564 public void actionPerformed(ActionEvent e)
1566 hiddenMarkers_actionPerformed(e);
1570 JMenuItem invertColSel = new JMenuItem(
1571 MessageManager.getString("action.invert_column_selection"));
1572 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1573 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1574 | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1576 al = new ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 invertColSel_actionPerformed(e);
1584 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1586 showComplementMenuItem.setVisible(false);
1587 showComplementMenuItem.addActionListener(new ActionListener()
1590 public void actionPerformed(ActionEvent e)
1592 showComplement_actionPerformed(showComplementMenuItem.getState());
1596 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1599 public void stateChanged(ChangeEvent evt)
1601 JTabbedPane pane = (JTabbedPane) evt.getSource();
1602 int sel = pane.getSelectedIndex();
1603 tabSelectionChanged(sel);
1606 tabbedPane.addMouseListener(new MouseAdapter()
1609 public void mousePressed(MouseEvent e)
1611 if (e.isPopupTrigger()) // Mac
1613 tabbedPane_mousePressed(e);
1618 public void mouseReleased(MouseEvent e)
1620 if (e.isPopupTrigger()) // Windows
1622 tabbedPane_mousePressed(e);
1626 tabbedPane.addFocusListener(new FocusAdapter()
1629 public void focusGained(FocusEvent e)
1631 tabbedPane_focusGained(e);
1635 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1636 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1637 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1638 al = new ActionListener()
1641 public void actionPerformed(ActionEvent e)
1643 save_actionPerformed(e);
1646 addMenuActionAndAccelerator(keyStroke, save, al);
1648 reload.setEnabled(false);
1649 reload.setText(MessageManager.getString("action.reload"));
1650 reload.addActionListener(new ActionListener()
1653 public void actionPerformed(ActionEvent e)
1655 reload_actionPerformed(e);
1659 JMenuItem newView = new JMenuItem(
1660 MessageManager.getString("action.new_view"));
1661 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1662 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1663 al = new ActionListener()
1666 public void actionPerformed(ActionEvent e)
1668 newView_actionPerformed(e);
1671 addMenuActionAndAccelerator(keyStroke, newView, al);
1673 tabbedPane.setToolTipText("<html><i>"
1674 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1677 formatMenu.setText(MessageManager.getString("action.format"));
1678 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1680 idRightAlign.setText(
1681 MessageManager.getString("label.right_align_sequence_id"));
1682 idRightAlign.addActionListener(new ActionListener()
1685 public void actionPerformed(ActionEvent e)
1687 idRightAlign_actionPerformed(e);
1691 gatherViews.setEnabled(false);
1692 gatherViews.setText(MessageManager.getString("action.gather_views"));
1693 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1694 al = new ActionListener()
1697 public void actionPerformed(ActionEvent e)
1699 gatherViews_actionPerformed(e);
1702 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1704 expandViews.setEnabled(false);
1705 expandViews.setText(MessageManager.getString("action.expand_views"));
1706 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1707 al = new ActionListener()
1710 public void actionPerformed(ActionEvent e)
1712 expandViews_actionPerformed(e);
1715 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1717 JMenuItem pageSetup = new JMenuItem(
1718 MessageManager.getString("action.page_setup"));
1719 pageSetup.addActionListener(new ActionListener()
1722 public void actionPerformed(ActionEvent e)
1724 pageSetup_actionPerformed(e);
1727 JMenuItem alignmentProperties = new JMenuItem(
1728 MessageManager.getString("label.alignment_props"));
1729 alignmentProperties.addActionListener(new ActionListener()
1732 public void actionPerformed(ActionEvent actionEvent)
1734 alignmentProperties();
1737 JMenuItem selectHighlighted = new JMenuItem(
1738 MessageManager.getString("action.select_highlighted_columns"));
1739 selectHighlighted.setToolTipText(
1740 MessageManager.getString("tooltip.select_highlighted_columns"));
1741 al = new ActionListener()
1744 public void actionPerformed(ActionEvent actionEvent)
1746 selectHighlightedColumns_actionPerformed(actionEvent);
1749 selectHighlighted.addActionListener(al);
1750 JMenu tooltipSettingsMenu = new JMenu(
1751 MessageManager.getString("label.sequence_id_tooltip"));
1752 JMenu autoAnnMenu = new JMenu(
1753 MessageManager.getString("label.autocalculated_annotation"));
1755 JMenu exportImageMenu = new JMenu(
1756 MessageManager.getString("label.export_image"));
1757 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1758 alignFrameMenuBar.add(fileMenu);
1759 alignFrameMenuBar.add(editMenu);
1760 alignFrameMenuBar.add(selectMenu);
1761 alignFrameMenuBar.add(viewMenu);
1762 alignFrameMenuBar.add(annotationsMenu);
1763 alignFrameMenuBar.add(calculateMenu);
1764 alignFrameMenuBar.add(formatMenu);
1765 alignFrameMenuBar.add(colourMenu);
1766 if (!Platform.isJS())
1768 alignFrameMenuBar.add(webService);
1771 fileMenu.add(fetchSequence);
1772 fileMenu.add(addSequenceMenu);
1773 fileMenu.add(reload);
1774 fileMenu.addSeparator();
1775 fileMenu.add(vamsasStore);
1777 fileMenu.add(saveAs);
1778 fileMenu.add(outputTextboxMenu);
1779 fileMenu.add(pageSetup);
1780 fileMenu.add(printMenuItem);
1781 fileMenu.addSeparator();
1782 fileMenu.add(exportImageMenu);
1783 fileMenu.add(exportFeatures);
1784 fileMenu.add(exportAnnotations);
1785 fileMenu.add(loadTreeMenuItem);
1786 fileMenu.add(associatedData);
1787 if (!Platform.isJS())
1789 fileMenu.add(loadVcf);
1791 fileMenu.addSeparator();
1792 fileMenu.add(closeMenuItem);
1794 pasteMenu.add(pasteNew);
1795 pasteMenu.add(pasteThis);
1796 editMenu.add(undoMenuItem);
1797 editMenu.add(redoMenuItem);
1800 editMenu.add(pasteMenu);
1801 editMenu.add(delete);
1802 editMenu.addSeparator();
1803 editMenu.add(remove2LeftMenuItem);
1804 editMenu.add(remove2RightMenuItem);
1805 editMenu.add(removeGappedColumnMenuItem);
1806 editMenu.add(removeAllGapsMenuItem);
1807 editMenu.add(removeRedundancyMenuItem);
1808 editMenu.addSeparator();
1809 // dont add these yet in the CVS build - they cannot be undone!
1810 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1811 // editMenu.add(justifyLeftMenuItem);
1812 // editMenu.add(justifyRightMenuItem);
1813 // editMenu.addSeparator();
1814 editMenu.add(padGapsMenuitem);
1816 showMenu.add(showAllColumns);
1817 showMenu.add(showAllSeqs);
1818 showMenu.add(showAllhidden);
1819 hideMenu.add(hideSelColumns);
1820 hideMenu.add(hideSelSequences);
1821 hideMenu.add(hideAllSelection);
1822 hideMenu.add(hideAllButSelection);
1823 viewMenu.add(newView);
1824 viewMenu.add(expandViews);
1825 viewMenu.add(gatherViews);
1826 viewMenu.addSeparator();
1827 viewMenu.add(showMenu);
1828 viewMenu.add(hideMenu);
1829 viewMenu.add(showComplementMenuItem);
1830 viewMenu.addSeparator();
1831 viewMenu.add(followHighlightMenuItem);
1832 viewMenu.addSeparator();
1833 viewMenu.add(showSeqFeatures);
1834 // viewMenu.add(showSeqFeaturesHeight);
1835 viewMenu.add(openFeatureSettings);
1836 tooltipSettingsMenu.add(showDbRefsMenuitem);
1837 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1838 viewMenu.add(tooltipSettingsMenu);
1839 viewMenu.addSeparator();
1840 viewMenu.add(alignmentProperties);
1841 viewMenu.addSeparator();
1842 viewMenu.add(overviewMenuItem);
1844 annotationsMenu.add(annotationPanelMenuItem);
1845 annotationsMenu.addSeparator();
1846 annotationsMenu.add(showAllAlAnnotations);
1847 annotationsMenu.add(hideAllAlAnnotations);
1848 annotationsMenu.addSeparator();
1849 annotationsMenu.add(showAllSeqAnnotations);
1850 annotationsMenu.add(hideAllSeqAnnotations);
1851 annotationsMenu.add(sortAnnBySequence);
1852 annotationsMenu.add(sortAnnByLabel);
1853 annotationsMenu.addSeparator();
1854 autoAnnMenu.add(showAutoFirst);
1855 autoAnnMenu.add(showAutoLast);
1856 autoAnnMenu.addSeparator();
1857 autoAnnMenu.add(applyAutoAnnotationSettings);
1858 autoAnnMenu.add(showConsensusHistogram);
1859 autoAnnMenu.add(showSequenceLogo);
1860 autoAnnMenu.add(normaliseSequenceLogo);
1861 autoAnnMenu.addSeparator();
1862 autoAnnMenu.add(showGroupConservation);
1863 autoAnnMenu.add(showGroupConsensus);
1864 annotationsMenu.add(autoAnnMenu);
1866 sort.add(sortIDMenuItem);
1867 sort.add(sortLengthMenuItem);
1868 sort.add(sortGroupMenuItem);
1869 sort.add(sortPairwiseMenuItem);
1870 sort.add(sortByTreeMenu);
1871 calculateMenu.add(sort);
1872 calculateMenu.add(calculateTree);
1873 calculateMenu.addSeparator();
1874 calculateMenu.add(pairwiseAlignmentMenuItem);
1875 calculateMenu.addSeparator();
1876 calculateMenu.add(showTranslation);
1877 calculateMenu.add(showReverse);
1878 calculateMenu.add(showReverseComplement);
1879 calculateMenu.add(showProducts);
1880 calculateMenu.add(autoCalculate);
1881 calculateMenu.add(sortByTree);
1882 calculateMenu.addSeparator();
1883 calculateMenu.add(expandAlignment);
1884 calculateMenu.add(extractScores);
1885 if (!Platform.isJS())
1887 calculateMenu.addSeparator();
1888 calculateMenu.add(runGroovy);
1891 webServiceNoServices = new JMenuItem(
1892 MessageManager.getString("label.no_services"));
1893 webService.add(webServiceNoServices);
1894 if (!Platform.isJS())
1896 exportImageMenu.add(htmlMenuItem);
1898 exportImageMenu.add(epsFile);
1899 exportImageMenu.add(createPNG);
1900 if (!Platform.isJS())
1902 exportImageMenu.add(createBioJS);
1903 exportImageMenu.add(createSVG);
1905 addSequenceMenu.add(addFromFile);
1906 addSequenceMenu.add(addFromText);
1907 addSequenceMenu.add(addFromURL);
1908 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1909 statusPanel.add(statusBar, null);
1910 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1912 formatMenu.add(font);
1913 formatMenu.addSeparator();
1914 formatMenu.add(wrapMenuItem);
1915 formatMenu.add(scaleAbove);
1916 formatMenu.add(scaleLeft);
1917 formatMenu.add(scaleRight);
1918 formatMenu.add(seqLimits);
1919 formatMenu.add(idRightAlign);
1920 formatMenu.add(hiddenMarkers);
1921 formatMenu.add(viewBoxesMenuItem);
1922 formatMenu.add(viewTextMenuItem);
1923 formatMenu.add(colourTextMenuItem);
1924 formatMenu.add(renderGapsMenuItem);
1925 formatMenu.add(centreColumnLabelsMenuItem);
1926 formatMenu.add(showNonconservedMenuItem);
1927 selectMenu.add(findMenuItem);
1928 selectMenu.addSeparator();
1929 selectMenu.add(selectAllSequenceMenuItem);
1930 selectMenu.add(deselectAllSequenceMenuItem);
1931 selectMenu.add(invertSequenceMenuItem);
1932 selectMenu.add(invertColSel);
1933 selectMenu.add(createGroup);
1934 selectMenu.add(unGroup);
1935 selectMenu.add(grpsFromSelection);
1936 selectMenu.add(deleteGroups);
1937 selectMenu.add(annotationColumn);
1938 selectMenu.add(selectHighlighted);
1939 // TODO - determine if the listenToViewSelections button is needed : see bug
1941 // selectMenu.addSeparator();
1942 // selectMenu.add(listenToViewSelections);
1945 protected void enableSortMenuOptions()
1949 protected void loadVcf_actionPerformed()
1954 * Constructs the entries on the Colour menu (but does not add them to the
1957 protected void initColourMenu()
1959 applyToAllGroups = new JCheckBoxMenuItem(
1960 MessageManager.getString("label.apply_colour_to_all_groups"));
1961 applyToAllGroups.addActionListener(new ActionListener()
1964 public void actionPerformed(ActionEvent e)
1966 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1970 textColour = new JMenuItem(
1971 MessageManager.getString("label.text_colour"));
1972 textColour.addActionListener(new ActionListener()
1975 public void actionPerformed(ActionEvent e)
1977 textColour_actionPerformed();
1981 conservationMenuItem = new JCheckBoxMenuItem(
1982 MessageManager.getString("action.by_conservation"));
1983 conservationMenuItem.addActionListener(new ActionListener()
1986 public void actionPerformed(ActionEvent e)
1988 conservationMenuItem_actionPerformed(
1989 conservationMenuItem.isSelected());
1993 abovePIDThreshold = new JCheckBoxMenuItem(
1994 MessageManager.getString("label.above_identity_threshold"));
1995 abovePIDThreshold.addActionListener(new ActionListener()
1998 public void actionPerformed(ActionEvent e)
2000 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2003 modifyPID = new JMenuItem(
2004 MessageManager.getString("label.modify_identity_threshold"));
2005 modifyPID.addActionListener(new ActionListener()
2008 public void actionPerformed(ActionEvent e)
2010 modifyPID_actionPerformed();
2013 modifyConservation = new JMenuItem(MessageManager
2014 .getString("label.modify_conservation_threshold"));
2015 modifyConservation.addActionListener(new ActionListener()
2018 public void actionPerformed(ActionEvent e)
2020 modifyConservation_actionPerformed();
2024 annotationColour = new JRadioButtonMenuItem(
2025 MessageManager.getString("action.by_annotation"));
2026 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2027 annotationColour.addActionListener(new ActionListener()
2030 public void actionPerformed(ActionEvent e)
2032 annotationColour_actionPerformed();
2037 protected void selectHighlightedColumns_actionPerformed(
2038 ActionEvent actionEvent)
2040 // TODO Auto-generated method stub
2045 * Generate the reverse sequence (or reverse complement if the flag is true)
2046 * and add it to the alignment
2050 protected void showReverse_actionPerformed(boolean complement)
2055 * Try to run script in a Groovy console, having first ensured that this
2056 * alignframe is set as currentAlignFrame in Desktop
2058 protected void runGroovy_actionPerformed()
2064 * Adds the given action listener and key accelerator to the given menu item.
2065 * Also saves in a lookup table to support lookup of action by key stroke.
2069 * @param actionListener
2071 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2072 JMenuItem menuItem, ActionListener actionListener)
2074 menuItem.setAccelerator(keyStroke);
2075 accelerators.put(keyStroke, menuItem);
2076 menuItem.addActionListener(actionListener);
2080 * Action on clicking sort annotations by type.
2084 protected void sortAnnotations_actionPerformed()
2089 * Action on clicking Show all annotations.
2091 * @param forSequences
2092 * update sequence-related annotations
2093 * @param forAlignment
2094 * update non-sequence-related annotations
2096 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2097 boolean forAlignment)
2099 setAnnotationsVisibility(true, forSequences, forAlignment);
2103 * Action on clicking Hide all annotations.
2105 * @param forSequences
2106 * update sequence-related annotations
2107 * @param forAlignment
2108 * update non-sequence-related annotations
2110 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2111 boolean forAlignment)
2113 setAnnotationsVisibility(false, forSequences, forAlignment);
2117 * Set the visibility of annotations to true or false. Can act on
2118 * sequence-related annotations, or alignment-related, or both.
2121 * @param forSequences
2122 * update sequence-related annotations
2123 * @param forAlignment
2124 * update non-sequence-related annotations
2126 protected void setAnnotationsVisibility(boolean visible,
2127 boolean forSequences, boolean forAlignment)
2132 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2134 // TODO Auto-generated method stub
2138 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2140 // TODO Auto-generated method stub
2144 protected void showAllhidden_actionPerformed(ActionEvent e)
2146 // TODO Auto-generated method stub
2150 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2152 // TODO Auto-generated method stub
2156 protected void hideAllSelection_actionPerformed(ActionEvent e)
2158 // TODO Auto-generated method stub
2162 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2164 // TODO Auto-generated method stub
2168 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2170 // TODO Auto-generated method stub
2174 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2176 // TODO Auto-generated method stub
2180 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2182 // TODO Auto-generated method stub
2186 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2188 // TODO Auto-generated method stub
2192 protected void showGroupConservation_actionPerformed(ActionEvent e)
2194 // TODO Auto-generated method stub
2198 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2200 // TODO Auto-generated method stub
2204 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2206 // TODO Auto-generated method stub
2210 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2212 // TODO Auto-generated method stub
2216 protected void followHighlight_actionPerformed()
2218 // TODO Auto-generated method stub
2222 protected void showNpFeats_actionPerformed(ActionEvent e)
2224 // TODO Auto-generated method stub
2228 protected void showDbRefs_actionPerformed(ActionEvent e)
2230 // TODO Auto-generated method stub
2234 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2238 protected void buildSortByAnnotationScoresMenu()
2242 protected void extractScores_actionPerformed(ActionEvent e)
2246 protected void outputText_actionPerformed(String formatName)
2250 public void addFromFile_actionPerformed(ActionEvent e)
2255 public void addFromText_actionPerformed(ActionEvent e)
2260 public void addFromURL_actionPerformed(ActionEvent e)
2265 public void exportFeatures_actionPerformed(ActionEvent e)
2270 public void exportAnnotations_actionPerformed(ActionEvent e)
2275 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2279 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2284 protected void closeMenuItem_actionPerformed(boolean b)
2288 protected void redoMenuItem_actionPerformed(ActionEvent e)
2292 protected void undoMenuItem_actionPerformed(ActionEvent e)
2296 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2300 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2304 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2308 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2312 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2316 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2320 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2324 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2328 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2332 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2336 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2340 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2344 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2348 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2352 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2356 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2360 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2364 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2368 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2372 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2376 protected void conservationMenuItem_actionPerformed(boolean selected)
2380 protected void printMenuItem_actionPerformed(ActionEvent e)
2384 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2388 protected void findMenuItem_actionPerformed(ActionEvent e)
2392 protected void abovePIDThreshold_actionPerformed(boolean selected)
2396 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2400 protected void deleteGroups_actionPerformed(ActionEvent e)
2404 protected void createGroup_actionPerformed(ActionEvent e)
2408 protected void unGroup_actionPerformed(ActionEvent e)
2412 protected void copy_actionPerformed()
2416 protected void cut_actionPerformed()
2420 protected void delete_actionPerformed()
2424 protected void pasteNew_actionPerformed(ActionEvent e)
2428 protected void pasteThis_actionPerformed(ActionEvent e)
2432 protected void applyToAllGroups_actionPerformed(boolean selected)
2436 public void createPNG(java.io.File f)
2440 protected void font_actionPerformed(ActionEvent e)
2444 protected void seqLimit_actionPerformed(ActionEvent e)
2448 public void seqDBRef_actionPerformed(ActionEvent e)
2453 public void createEPS(java.io.File f)
2457 public void createSVG(java.io.File f)
2462 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2468 * Template method to handle the 'load T-Coffee scores' menu event.
2470 * Subclasses override this method to provide a custom action.
2475 protected void loadScores_actionPerformed(ActionEvent event)
2480 protected void jpred_actionPerformed(ActionEvent e)
2484 protected void scaleAbove_actionPerformed(ActionEvent e)
2488 protected void scaleLeft_actionPerformed(ActionEvent e)
2492 protected void scaleRight_actionPerformed(ActionEvent e)
2496 protected void modifyPID_actionPerformed()
2500 protected void modifyConservation_actionPerformed()
2504 protected void saveAs_actionPerformed()
2508 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2512 public void vamsasStore_actionPerformed(ActionEvent e)
2517 public void vamsasLoad_actionPerformed(ActionEvent e)
2522 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2527 public void featureSettings_actionPerformed(ActionEvent e)
2532 public void fetchSequence_actionPerformed()
2537 public void smoothFont_actionPerformed(ActionEvent e)
2542 public void annotationColour_actionPerformed()
2546 public void annotationColumn_actionPerformed(ActionEvent e)
2550 public void associatedData_actionPerformed(ActionEvent e)
2555 public void autoCalculate_actionPerformed(ActionEvent e)
2560 public void sortByTreeOption_actionPerformed(ActionEvent e)
2565 public void showAllSeqs_actionPerformed(ActionEvent e)
2570 public void showAllColumns_actionPerformed(ActionEvent e)
2575 public void hideSelSequences_actionPerformed(ActionEvent e)
2580 public void hideSelColumns_actionPerformed(ActionEvent e)
2585 public void hiddenMarkers_actionPerformed(ActionEvent e)
2590 public void findPdbId_actionPerformed(ActionEvent e)
2595 public void enterPdbId_actionPerformed(ActionEvent e)
2600 public void pdbFile_actionPerformed(ActionEvent e)
2605 public void invertColSel_actionPerformed(ActionEvent e)
2610 public void tabSelectionChanged(int sel)
2615 public void tabbedPane_mousePressed(MouseEvent e)
2620 public void tabbedPane_focusGained(FocusEvent e)
2625 public void save_actionPerformed(ActionEvent e)
2630 public void reload_actionPerformed(ActionEvent e)
2635 public void newView_actionPerformed(ActionEvent e)
2640 public void textColour_actionPerformed()
2645 public void idRightAlign_actionPerformed(ActionEvent e)
2650 public void expandViews_actionPerformed(ActionEvent e)
2655 public void gatherViews_actionPerformed(ActionEvent e)
2660 public void buildTreeSortMenu()
2665 public void pageSetup_actionPerformed(ActionEvent e)
2670 public void alignmentProperties()
2675 protected void expand_newalign(ActionEvent e)
2677 // TODO Auto-generated method stub
2681 protected boolean isShowAutoCalculatedAbove()
2683 return showAutoCalculatedAbove;
2686 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2688 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2691 protected SequenceAnnotationOrder getAnnotationSortOrder()
2693 return annotationSortOrder;
2696 protected void setAnnotationSortOrder(
2697 SequenceAnnotationOrder annotationSortOrder)
2699 this.annotationSortOrder = annotationSortOrder;
2702 public Map<KeyStroke, JMenuItem> getAccelerators()
2704 return this.accelerators;
2708 * Returns the selected index of the tabbed pane, or -1 if none selected
2709 * (including the case where the tabbed pane has not been made visible).
2713 public int getTabIndex()
2715 return tabbedPane.getSelectedIndex();
2718 public JPanel getStatusPanel()
2724 * Sets a reference to the containing split frame. Also makes the 'toggle
2725 * split view' menu item visible and checked.
2729 public void setSplitFrame(SplitContainerI sf)
2731 this.splitFrame = sf;
2734 this.showComplementMenuItem.setVisible(true);
2735 this.showComplementMenuItem.setState(true);
2739 public SplitContainerI getSplitViewContainer()
2741 return this.splitFrame;
2744 protected void showComplement_actionPerformed(boolean complement)