2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.analysis.GeneticCodeI;
25 import jalview.analysis.GeneticCodes;
26 import jalview.api.SplitContainerI;
27 import jalview.bin.Cache;
28 import jalview.gui.JvSwingUtils;
29 import jalview.gui.Preferences;
30 import jalview.io.FileFormats;
31 import jalview.schemes.ResidueColourScheme;
32 import jalview.util.MessageManager;
33 import jalview.util.Platform;
35 import java.awt.BorderLayout;
36 import java.awt.Color;
37 import java.awt.GridLayout;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.event.FocusAdapter;
41 import java.awt.event.FocusEvent;
42 import java.awt.event.KeyEvent;
43 import java.awt.event.MouseAdapter;
44 import java.awt.event.MouseEvent;
45 import java.util.HashMap;
48 import javax.swing.BorderFactory;
49 import javax.swing.ButtonGroup;
50 import javax.swing.JCheckBoxMenuItem;
51 import javax.swing.JInternalFrame;
52 import javax.swing.JLabel;
53 import javax.swing.JMenu;
54 import javax.swing.JMenuBar;
55 import javax.swing.JMenuItem;
56 import javax.swing.JPanel;
57 import javax.swing.JRadioButtonMenuItem;
58 import javax.swing.JTabbedPane;
59 import javax.swing.KeyStroke;
60 import javax.swing.event.ChangeEvent;
61 import javax.swing.event.MenuEvent;
62 import javax.swing.event.MenuListener;
64 @SuppressWarnings("serial")
65 public class GAlignFrame extends JInternalFrame
67 protected JMenuBar alignFrameMenuBar = new JMenuBar();
69 protected JMenuItem closeMenuItem = new JMenuItem();
71 public JMenu webService = new JMenu();// BH 2019 was protected, but not
72 // sufficient for AlignFrame thread run
74 public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
75 // sufficient for AlignFrame thread run
77 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
79 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
81 protected JMenu sortByAnnotScore = new JMenu();
83 public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
85 // AlignFrame.printWriter
87 protected JMenu outputTextboxMenu = new JMenu();
89 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
91 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
93 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
95 protected JMenuItem undoMenuItem = new JMenuItem();
97 protected JMenuItem redoMenuItem = new JMenuItem();
99 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
101 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
103 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
105 JMenuItem copy = new JMenuItem();
107 JMenuItem cut = new JMenuItem();
109 JMenu pasteMenu = new JMenu();
111 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
113 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
115 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
117 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
119 protected JCheckBoxMenuItem applyToAllGroups;
121 protected JMenu colourMenu = new JMenu();
123 protected JMenuItem textColour;
125 protected JCheckBoxMenuItem conservationMenuItem;
127 protected JMenuItem modifyConservation;
129 protected JCheckBoxMenuItem abovePIDThreshold;
131 protected JMenuItem modifyPID;
133 protected JRadioButtonMenuItem annotationColour;
135 protected JMenu sortByTreeMenu = new JMenu();
137 protected JMenu sort = new JMenu();
139 protected JMenuItem calculateTree = new JMenuItem();
141 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
143 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
145 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
147 protected JMenu showTranslation = new JMenu();
149 protected JMenuItem showReverse = new JMenuItem();
151 protected JMenuItem showReverseComplement = new JMenuItem();
153 protected JMenu showProducts = new JMenu();
155 protected JMenuItem runGroovy = new JMenuItem();
157 protected JMenuItem loadVcf;
159 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
161 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
163 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
165 protected JPanel statusPanel = new JPanel();
167 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
169 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
171 protected JMenuItem showAllAlAnnotations = new JMenuItem();
173 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
175 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
177 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
179 protected JTabbedPane tabbedPane = new JTabbedPane();
181 protected JMenuItem reload = new JMenuItem();
183 protected JMenu formatMenu = new JMenu();
185 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
187 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
189 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
191 protected JMenuItem gatherViews = new JMenuItem();
193 protected JMenuItem expandViews = new JMenuItem();
195 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
203 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
207 protected JMenuItem openFeatureSettings;
209 private SequenceAnnotationOrder annotationSortOrder;
211 private boolean showAutoCalculatedAbove = false;
213 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
215 private SplitContainerI splitFrame;
222 // for Web-page embedding using id=align-frame-div
223 setName("jalview-alignment");
226 setJMenuBar(alignFrameMenuBar);
228 // dynamically fill save as menu with available formats
229 for (String ff : FileFormats.getInstance().getWritableFormats(true))
231 JMenuItem item = new JMenuItem(ff);
233 item.addActionListener(new ActionListener()
236 public void actionPerformed(ActionEvent e)
238 outputText_actionPerformed(e.getActionCommand());
242 outputTextboxMenu.add(item);
244 } catch (Exception e)
246 System.err.println(e.toString());
249 if (Platform.allowMnemonics()) // was "not mac and not JS"
251 closeMenuItem.setMnemonic('C');
252 outputTextboxMenu.setMnemonic('T');
253 undoMenuItem.setMnemonic('Z');
254 redoMenuItem.setMnemonic('0');
255 copy.setMnemonic('C');
256 cut.setMnemonic('U');
257 pasteMenu.setMnemonic('P');
258 reload.setMnemonic('R');
262 private void jbInit() throws Exception
266 JMenuItem saveAs = new JMenuItem(
267 MessageManager.getString("action.save_as"));
268 ActionListener al = new ActionListener()
271 public void actionPerformed(ActionEvent e)
273 saveAs_actionPerformed();
277 // FIXME getDefaultToolkit throws an exception in Headless mode
278 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
279 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
280 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
282 addMenuActionAndAccelerator(keyStroke, saveAs, al);
284 closeMenuItem.setText(MessageManager.getString("action.close"));
285 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
286 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
287 al = new ActionListener()
290 public void actionPerformed(ActionEvent e)
292 closeMenuItem_actionPerformed(false);
295 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
297 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
298 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
299 JMenu annotationsMenu = new JMenu(
300 MessageManager.getString("action.annotations"));
301 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
302 colourMenu.setText(MessageManager.getString("action.colour"));
303 JMenu calculateMenu = new JMenu(
304 MessageManager.getString("action.calculate"));
305 webService.setText(MessageManager.getString("action.web_service"));
306 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
307 MessageManager.getString("action.select_all"));
308 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
309 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
310 al = new ActionListener()
313 public void actionPerformed(ActionEvent e)
315 selectAllSequenceMenuItem_actionPerformed(e);
318 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
320 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
321 MessageManager.getString("action.deselect_all"));
322 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
323 al = new ActionListener()
326 public void actionPerformed(ActionEvent e)
328 deselectAllSequenceMenuItem_actionPerformed(e);
331 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
333 JMenuItem invertSequenceMenuItem = new JMenuItem(
334 MessageManager.getString("action.invert_sequence_selection"));
335 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
336 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
337 al = new ActionListener()
340 public void actionPerformed(ActionEvent e)
342 invertSequenceMenuItem_actionPerformed(e);
345 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
347 JMenuItem grpsFromSelection = new JMenuItem(
348 MessageManager.getString("action.make_groups_selection"));
349 grpsFromSelection.addActionListener(new ActionListener()
352 public void actionPerformed(ActionEvent e)
354 makeGrpsFromSelection_actionPerformed(e);
357 JMenuItem expandAlignment = new JMenuItem(
358 MessageManager.getString("action.view_flanking_regions"));
359 expandAlignment.setToolTipText(
360 MessageManager.getString("label.view_flanking_regions"));
361 expandAlignment.addActionListener(new ActionListener()
364 public void actionPerformed(ActionEvent e)
369 JMenuItem remove2LeftMenuItem = new JMenuItem(
370 MessageManager.getString("action.remove_left"));
371 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
372 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
373 al = new ActionListener()
376 public void actionPerformed(ActionEvent e)
378 remove2LeftMenuItem_actionPerformed(e);
381 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
383 JMenuItem remove2RightMenuItem = new JMenuItem(
384 MessageManager.getString("action.remove_right"));
385 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
386 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
387 al = new ActionListener()
390 public void actionPerformed(ActionEvent e)
392 remove2RightMenuItem_actionPerformed(e);
395 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
397 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
398 MessageManager.getString("action.remove_empty_columns"));
399 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
400 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
401 al = new ActionListener()
404 public void actionPerformed(ActionEvent e)
406 removeGappedColumnMenuItem_actionPerformed(e);
409 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
411 JMenuItem removeAllGapsMenuItem = new JMenuItem(
412 MessageManager.getString("action.remove_all_gaps"));
413 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
414 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
415 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
417 al = new ActionListener()
420 public void actionPerformed(ActionEvent e)
422 removeAllGapsMenuItem_actionPerformed(e);
425 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
427 JMenuItem justifyLeftMenuItem = new JMenuItem(
428 MessageManager.getString("action.left_justify_alignment"));
429 justifyLeftMenuItem.addActionListener(new ActionListener()
432 public void actionPerformed(ActionEvent e)
434 justifyLeftMenuItem_actionPerformed(e);
437 JMenuItem justifyRightMenuItem = new JMenuItem(
438 MessageManager.getString("action.right_justify_alignment"));
439 justifyRightMenuItem.addActionListener(new ActionListener()
442 public void actionPerformed(ActionEvent e)
444 justifyRightMenuItem_actionPerformed(e);
447 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
448 viewBoxesMenuItem.setState(true);
449 viewBoxesMenuItem.addActionListener(new ActionListener()
452 public void actionPerformed(ActionEvent e)
454 viewBoxesMenuItem_actionPerformed(e);
457 viewTextMenuItem.setText(MessageManager.getString("action.text"));
458 viewTextMenuItem.setState(true);
459 viewTextMenuItem.addActionListener(new ActionListener()
462 public void actionPerformed(ActionEvent e)
464 viewTextMenuItem_actionPerformed(e);
467 showNonconservedMenuItem
468 .setText(MessageManager.getString("label.show_non_conserved"));
469 showNonconservedMenuItem.setState(false);
470 showNonconservedMenuItem.addActionListener(new ActionListener()
473 public void actionPerformed(ActionEvent e)
475 showUnconservedMenuItem_actionPerformed(e);
478 JMenuItem sortPairwiseMenuItem = new JMenuItem(
479 MessageManager.getString("action.by_pairwise_id"));
480 sortPairwiseMenuItem.addActionListener(new ActionListener()
483 public void actionPerformed(ActionEvent e)
485 sortPairwiseMenuItem_actionPerformed(e);
488 JMenuItem sortIDMenuItem = new JMenuItem(
489 MessageManager.getString("action.by_id"));
490 sortIDMenuItem.addActionListener(new ActionListener()
493 public void actionPerformed(ActionEvent e)
495 sortIDMenuItem_actionPerformed(e);
498 JMenuItem sortLengthMenuItem = new JMenuItem(
499 MessageManager.getString("action.by_length"));
500 sortLengthMenuItem.addActionListener(new ActionListener()
503 public void actionPerformed(ActionEvent e)
505 sortLengthMenuItem_actionPerformed(e);
508 JMenuItem sortGroupMenuItem = new JMenuItem(
509 MessageManager.getString("action.by_group"));
510 sortGroupMenuItem.addActionListener(new ActionListener()
513 public void actionPerformed(ActionEvent e)
515 sortGroupMenuItem_actionPerformed(e);
519 JMenuItem removeRedundancyMenuItem = new JMenuItem(
520 MessageManager.getString("action.remove_redundancy"));
521 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
522 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
523 al = new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 removeRedundancyMenuItem_actionPerformed(e);
531 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
533 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
534 MessageManager.getString("action.pairwise_alignment"));
535 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
538 public void actionPerformed(ActionEvent e)
540 pairwiseAlignmentMenuItem_actionPerformed(e);
544 this.getContentPane().setLayout(new BorderLayout());
545 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
546 statusBar.setBackground(Color.white);
547 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
548 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
549 statusBar.setText(MessageManager.getString("label.status_bar"));
551 .setText(MessageManager.getString("label.out_to_textbox"));
553 annotationPanelMenuItem.setActionCommand("");
554 annotationPanelMenuItem
555 .setText(MessageManager.getString("label.show_annotations"));
556 annotationPanelMenuItem
557 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
558 annotationPanelMenuItem.addActionListener(new ActionListener()
561 public void actionPerformed(ActionEvent e)
563 annotationPanelMenuItem_actionPerformed(e);
566 showAllAlAnnotations.setText(
567 MessageManager.getString("label.show_all_al_annotations"));
568 final boolean isAnnotationPanelShown = annotationPanelMenuItem
570 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
571 showAllAlAnnotations.addActionListener(new ActionListener()
574 public void actionPerformed(ActionEvent e)
576 showAllAnnotations_actionPerformed(false, true);
579 hideAllAlAnnotations.setText(
580 MessageManager.getString("label.hide_all_al_annotations"));
581 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
582 hideAllAlAnnotations.addActionListener(new ActionListener()
585 public void actionPerformed(ActionEvent e)
587 hideAllAnnotations_actionPerformed(false, true);
590 showAllSeqAnnotations.setText(
591 MessageManager.getString("label.show_all_seq_annotations"));
592 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
593 showAllSeqAnnotations.addActionListener(new ActionListener()
596 public void actionPerformed(ActionEvent e)
598 showAllAnnotations_actionPerformed(true, false);
601 hideAllSeqAnnotations.setText(
602 MessageManager.getString("label.hide_all_seq_annotations"));
603 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
604 hideAllSeqAnnotations.addActionListener(new ActionListener()
607 public void actionPerformed(ActionEvent e)
609 hideAllAnnotations_actionPerformed(true, false);
612 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
613 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
614 SequenceAnnotationOrder.NONE.name()));
615 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
616 MessageManager.getString("label.sort_annotations_by_sequence"));
617 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
618 MessageManager.getString("label.sort_annotations_by_label"));
620 sortAnnBySequence.setSelected(
621 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
622 sortAnnBySequence.addActionListener(new ActionListener()
625 public void actionPerformed(ActionEvent e)
627 boolean newState = sortAnnBySequence.getState();
628 sortAnnByLabel.setSelected(false);
629 setAnnotationSortOrder(
630 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
631 : SequenceAnnotationOrder.NONE);
632 sortAnnotations_actionPerformed();
635 sortAnnByLabel.setSelected(
636 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
637 sortAnnByLabel.addActionListener(new ActionListener()
640 public void actionPerformed(ActionEvent e)
642 boolean newState = sortAnnByLabel.getState();
643 sortAnnBySequence.setSelected(false);
644 setAnnotationSortOrder(
645 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
646 : SequenceAnnotationOrder.NONE);
647 sortAnnotations_actionPerformed();
650 colourTextMenuItem = new JCheckBoxMenuItem(
651 MessageManager.getString("label.colour_text"));
652 colourTextMenuItem.addActionListener(new ActionListener()
655 public void actionPerformed(ActionEvent e)
657 colourTextMenuItem_actionPerformed(e);
661 JMenuItem htmlMenuItem = new JMenuItem(
662 MessageManager.getString("label.html"));
663 htmlMenuItem.addActionListener(new ActionListener()
666 public void actionPerformed(ActionEvent e)
668 htmlMenuItem_actionPerformed(e);
672 JMenuItem createBioJS = new JMenuItem(
673 MessageManager.getString("label.biojs_html_export"));
674 createBioJS.addActionListener(new java.awt.event.ActionListener()
677 public void actionPerformed(ActionEvent e)
679 bioJSMenuItem_actionPerformed(e);
683 JMenuItem overviewMenuItem = new JMenuItem(
684 MessageManager.getString("label.overview_window"));
685 overviewMenuItem.addActionListener(new ActionListener()
688 public void actionPerformed(ActionEvent e)
690 overviewMenuItem_actionPerformed(e);
694 undoMenuItem.setEnabled(false);
695 undoMenuItem.setText(MessageManager.getString("action.undo"));
696 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
697 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
698 al = new ActionListener()
701 public void actionPerformed(ActionEvent e)
703 undoMenuItem_actionPerformed(e);
706 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
708 redoMenuItem.setEnabled(false);
709 redoMenuItem.setText(MessageManager.getString("action.redo"));
710 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
711 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
712 al = new ActionListener()
715 public void actionPerformed(ActionEvent e)
717 redoMenuItem_actionPerformed(e);
720 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
722 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
723 wrapMenuItem.addActionListener(new ActionListener()
726 public void actionPerformed(ActionEvent e)
728 wrapMenuItem_actionPerformed(e);
732 JMenuItem printMenuItem = new JMenuItem(
733 MessageManager.getString("action.print"));
734 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
735 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
736 al = new ActionListener()
739 public void actionPerformed(ActionEvent e)
741 printMenuItem_actionPerformed(e);
744 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
747 .setText(MessageManager.getString("action.show_gaps"));
748 renderGapsMenuItem.setState(true);
749 renderGapsMenuItem.addActionListener(new ActionListener()
752 public void actionPerformed(ActionEvent e)
754 renderGapsMenuItem_actionPerformed(e);
758 JMenuItem findMenuItem = new JMenuItem(
759 MessageManager.getString("action.find"));
760 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
761 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
762 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
763 MessageManager.getString("label.find_tip")));
764 al = new ActionListener()
767 public void actionPerformed(ActionEvent e)
769 findMenuItem_actionPerformed(e);
772 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
774 showSeqFeatures.setText(
775 MessageManager.getString("label.show_sequence_features"));
776 showSeqFeatures.addActionListener(new ActionListener()
779 public void actionPerformed(ActionEvent actionEvent)
781 showSeqFeatures_actionPerformed(actionEvent);
785 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
786 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
787 * void actionPerformed(ActionEvent actionEvent) {
788 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
791 .setText(MessageManager.getString("label.show_database_refs"));
792 showDbRefsMenuitem.addActionListener(new ActionListener()
796 public void actionPerformed(ActionEvent e)
798 showDbRefs_actionPerformed(e);
802 showNpFeatsMenuitem.setText(
803 MessageManager.getString("label.show_non_positional_features"));
804 showNpFeatsMenuitem.addActionListener(new ActionListener()
808 public void actionPerformed(ActionEvent e)
810 showNpFeats_actionPerformed(e);
814 showGroupConservation
815 .setText(MessageManager.getString("label.group_conservation"));
816 showGroupConservation.addActionListener(new ActionListener()
820 public void actionPerformed(ActionEvent e)
822 showGroupConservation_actionPerformed(e);
828 .setText(MessageManager.getString("label.group_consensus"));
829 showGroupConsensus.addActionListener(new ActionListener()
833 public void actionPerformed(ActionEvent e)
835 showGroupConsensus_actionPerformed(e);
839 showConsensusHistogram.setText(
840 MessageManager.getString("label.show_consensus_histogram"));
841 showConsensusHistogram.addActionListener(new ActionListener()
845 public void actionPerformed(ActionEvent e)
847 showConsensusHistogram_actionPerformed(e);
852 .setText(MessageManager.getString("label.show_consensus_logo"));
853 showSequenceLogo.addActionListener(new ActionListener()
857 public void actionPerformed(ActionEvent e)
859 showSequenceLogo_actionPerformed(e);
863 normaliseSequenceLogo
864 .setText(MessageManager.getString("label.norm_consensus_logo"));
865 normaliseSequenceLogo.addActionListener(new ActionListener()
869 public void actionPerformed(ActionEvent e)
871 normaliseSequenceLogo_actionPerformed(e);
875 applyAutoAnnotationSettings
876 .setText(MessageManager.getString("label.apply_all_groups"));
877 applyAutoAnnotationSettings.setState(false);
878 applyAutoAnnotationSettings.setVisible(true);
879 applyAutoAnnotationSettings.addActionListener(new ActionListener()
882 public void actionPerformed(ActionEvent e)
884 applyAutoAnnotationSettings_actionPerformed(e);
888 ButtonGroup buttonGroup = new ButtonGroup();
889 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
890 MessageManager.getString("label.show_first"));
891 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
892 MessageManager.getString("label.show_last"));
893 buttonGroup.add(showAutoFirst);
894 buttonGroup.add(showAutoLast);
895 final boolean autoFirst = Cache
896 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
897 showAutoFirst.setSelected(autoFirst);
898 setShowAutoCalculatedAbove(autoFirst);
899 showAutoFirst.addActionListener(new ActionListener()
902 public void actionPerformed(ActionEvent e)
904 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
905 sortAnnotations_actionPerformed();
908 showAutoLast.setSelected(!showAutoFirst.isSelected());
909 showAutoLast.addActionListener(new ActionListener()
912 public void actionPerformed(ActionEvent e)
914 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
915 sortAnnotations_actionPerformed();
919 JMenuItem deleteGroups = new JMenuItem(
920 MessageManager.getString("action.undefine_groups"));
921 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
922 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
923 al = new ActionListener()
926 public void actionPerformed(ActionEvent e)
928 deleteGroups_actionPerformed(e);
931 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
933 JMenuItem annotationColumn = new JMenuItem(
934 MessageManager.getString("action.select_by_annotation"));
935 annotationColumn.addActionListener(new ActionListener()
938 public void actionPerformed(ActionEvent e)
940 annotationColumn_actionPerformed(e);
944 JMenuItem createGroup = new JMenuItem(
945 MessageManager.getString("action.create_group"));
946 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
947 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
948 al = new ActionListener()
951 public void actionPerformed(ActionEvent e)
953 createGroup_actionPerformed(e);
956 addMenuActionAndAccelerator(keyStroke, createGroup, al);
958 JMenuItem unGroup = new JMenuItem(
959 MessageManager.getString("action.remove_group"));
960 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
961 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
962 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
964 al = new ActionListener()
967 public void actionPerformed(ActionEvent e)
969 unGroup_actionPerformed(e);
972 addMenuActionAndAccelerator(keyStroke, unGroup, al);
974 copy.setText(MessageManager.getString("action.copy"));
975 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
976 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
978 al = new ActionListener()
981 public void actionPerformed(ActionEvent e)
983 copy_actionPerformed();
986 addMenuActionAndAccelerator(keyStroke, copy, al);
988 cut.setText(MessageManager.getString("action.cut"));
989 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
990 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
991 al = new ActionListener()
994 public void actionPerformed(ActionEvent e)
996 cut_actionPerformed();
999 addMenuActionAndAccelerator(keyStroke, cut, al);
1001 JMenuItem delete = new JMenuItem(
1002 MessageManager.getString("action.delete"));
1003 delete.addActionListener(new ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 delete_actionPerformed();
1012 pasteMenu.setText(MessageManager.getString("action.paste"));
1013 JMenuItem pasteNew = new JMenuItem(
1014 MessageManager.getString("label.to_new_alignment"));
1015 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1016 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1017 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1019 al = new ActionListener()
1022 public void actionPerformed(ActionEvent e)
1024 pasteNew_actionPerformed(e);
1027 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1029 JMenuItem pasteThis = new JMenuItem(
1030 MessageManager.getString("label.to_this_alignment"));
1031 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1032 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1033 al = new ActionListener()
1036 public void actionPerformed(ActionEvent e)
1038 pasteThis_actionPerformed(e);
1041 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1043 JMenuItem createPNG = new JMenuItem("PNG");
1044 createPNG.addActionListener(new ActionListener()
1047 public void actionPerformed(ActionEvent e)
1052 createPNG.setActionCommand(
1053 MessageManager.getString("label.save_png_image"));
1055 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1056 font.addActionListener(new ActionListener()
1059 public void actionPerformed(ActionEvent e)
1061 font_actionPerformed(e);
1065 MessageManager.getString("label.show_sequence_limits"));
1066 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1067 seqLimits.addActionListener(new ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 seqLimit_actionPerformed(e);
1075 JMenuItem epsFile = new JMenuItem("EPS");
1076 epsFile.addActionListener(new ActionListener()
1079 public void actionPerformed(ActionEvent e)
1085 JMenuItem createSVG = new JMenuItem("SVG");
1086 createSVG.addActionListener(new ActionListener()
1089 public void actionPerformed(ActionEvent e)
1095 JMenuItem loadTreeMenuItem = new JMenuItem(
1096 MessageManager.getString("label.load_associated_tree"));
1097 loadTreeMenuItem.setActionCommand(
1098 MessageManager.getString("label.load_tree_for_sequence_set"));
1099 loadTreeMenuItem.addActionListener(new ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 loadTreeMenuItem_actionPerformed(e);
1108 scaleAbove.setVisible(false);
1109 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1110 scaleAbove.addActionListener(new ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 scaleAbove_actionPerformed(e);
1118 scaleLeft.setVisible(false);
1119 scaleLeft.setSelected(true);
1120 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1121 scaleLeft.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 scaleLeft_actionPerformed(e);
1129 scaleRight.setVisible(false);
1130 scaleRight.setSelected(true);
1131 scaleRight.setText(MessageManager.getString("action.scale_right"));
1132 scaleRight.addActionListener(new ActionListener()
1135 public void actionPerformed(ActionEvent e)
1137 scaleRight_actionPerformed(e);
1140 centreColumnLabelsMenuItem.setVisible(true);
1141 centreColumnLabelsMenuItem.setState(false);
1142 centreColumnLabelsMenuItem.setText(
1143 MessageManager.getString("label.centre_column_labels"));
1144 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent e)
1149 centreColumnLabels_actionPerformed(e);
1152 followHighlightMenuItem.setVisible(true);
1153 followHighlightMenuItem.setState(true);
1154 followHighlightMenuItem
1155 .setText(MessageManager.getString("label.automatic_scrolling"));
1156 followHighlightMenuItem.addActionListener(new ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 followHighlight_actionPerformed();
1168 .setText(MessageManager.getString("action.by_tree_order"));
1169 sort.setText(MessageManager.getString("action.sort"));
1170 sort.addMenuListener(new MenuListener()
1173 public void menuSelected(MenuEvent e)
1175 buildTreeSortMenu();
1179 public void menuDeselected(MenuEvent e)
1184 public void menuCanceled(MenuEvent e)
1189 .setText(MessageManager.getString("label.sort_by_score"));
1190 sort.add(sortByAnnotScore);
1191 sort.addMenuListener(new javax.swing.event.MenuListener()
1195 public void menuCanceled(MenuEvent e)
1200 public void menuDeselected(MenuEvent e)
1205 public void menuSelected(MenuEvent e)
1207 buildSortByAnnotationScoresMenu();
1210 sortByAnnotScore.setVisible(false);
1213 .setText(MessageManager.getString("action.calculate_tree_pca"));
1215 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1217 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1218 padGapsMenuitem.addActionListener(new ActionListener()
1221 public void actionPerformed(ActionEvent e)
1223 padGapsMenuitem_actionPerformed(e);
1226 JMenuItem vamsasStore = new JMenuItem(
1227 MessageManager.getString("label.vamsas_store"));
1228 vamsasStore.setVisible(false);
1229 vamsasStore.addActionListener(new ActionListener()
1232 public void actionPerformed(ActionEvent e)
1234 vamsasStore_actionPerformed(e);
1239 * Translate as cDNA with sub-menu of translation tables
1242 .setText(MessageManager.getString("label.translate_cDNA"));
1243 boolean first = true;
1244 for (final GeneticCodeI table : GeneticCodes.getInstance()
1247 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1248 showTranslation.add(item);
1249 item.addActionListener(new ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 showTranslation_actionPerformed(table);
1259 showTranslation.addSeparator();
1264 showReverse.setText(MessageManager.getString("label.reverse"));
1265 showReverse.addActionListener(new ActionListener()
1268 public void actionPerformed(ActionEvent e)
1270 showReverse_actionPerformed(false);
1273 showReverseComplement
1274 .setText(MessageManager.getString("label.reverse_complement"));
1275 showReverseComplement.addActionListener(new ActionListener()
1278 public void actionPerformed(ActionEvent e)
1280 showReverse_actionPerformed(true);
1284 JMenuItem extractScores = new JMenuItem(
1285 MessageManager.getString("label.extract_scores"));
1286 extractScores.addActionListener(new ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 extractScores_actionPerformed(e);
1294 extractScores.setVisible(true);
1295 // JBPNote: TODO: make gui for regex based score extraction
1297 // for show products actions see AlignFrame.canShowProducts
1298 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1300 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1301 runGroovy.setToolTipText(
1302 MessageManager.getString("label.run_groovy_tip"));
1303 runGroovy.addActionListener(new ActionListener()
1306 public void actionPerformed(ActionEvent e)
1308 runGroovy_actionPerformed();
1312 openFeatureSettings = new JMenuItem(
1313 MessageManager.getString("action.feature_settings"));
1314 openFeatureSettings.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent e)
1319 featureSettings_actionPerformed(e);
1324 * add sub-menu of database we can fetch from
1326 JMenuItem fetchSequence = new JMenuItem(
1327 MessageManager.getString("label.fetch_sequences"));
1328 fetchSequence.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 fetchSequence_actionPerformed();
1337 JMenuItem associatedData = new JMenuItem(
1338 MessageManager.getString("label.load_features_annotations"));
1339 associatedData.addActionListener(new ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 associatedData_actionPerformed(e);
1347 loadVcf = new JMenuItem(
1348 MessageManager.getString("label.load_vcf_file"));
1349 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1350 loadVcf.addActionListener(new ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 loadVcf_actionPerformed();
1358 autoCalculate.setText(
1359 MessageManager.getString("label.autocalculate_consensus"));
1360 autoCalculate.setState(
1361 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1362 autoCalculate.addActionListener(new ActionListener()
1365 public void actionPerformed(ActionEvent e)
1367 autoCalculate_actionPerformed(e);
1371 MessageManager.getString("label.sort_alignment_new_tree"));
1372 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1373 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1375 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1376 sortByTree.addActionListener(new ActionListener()
1379 public void actionPerformed(ActionEvent e)
1381 sortByTreeOption_actionPerformed(e);
1385 listenToViewSelections.setText(
1386 MessageManager.getString("label.listen_for_selections"));
1387 listenToViewSelections
1388 .setToolTipText("<html>" + MessageManager.getString(
1389 "label.selections_mirror_selections_made_same_sequences_other_views"));
1390 listenToViewSelections.setState(false);
1391 listenToViewSelections.addActionListener(new ActionListener()
1394 public void actionPerformed(ActionEvent e)
1396 listenToViewSelections_actionPerformed(e);
1400 JMenu addSequenceMenu = new JMenu(
1401 MessageManager.getString("label.add_sequences"));
1402 JMenuItem addFromFile = new JMenuItem(
1403 MessageManager.getString("label.from_file"));
1404 addFromFile.addActionListener(new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 addFromFile_actionPerformed(e);
1412 JMenuItem addFromText = new JMenuItem(
1413 MessageManager.getString("label.from_textbox"));
1414 addFromText.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent e)
1419 addFromText_actionPerformed(e);
1422 JMenuItem addFromURL = new JMenuItem(
1423 MessageManager.getString("label.from_url"));
1424 addFromURL.addActionListener(new ActionListener()
1427 public void actionPerformed(ActionEvent e)
1429 addFromURL_actionPerformed(e);
1432 JMenuItem exportFeatures = new JMenuItem(
1433 MessageManager.getString("label.export_features"));
1434 exportFeatures.addActionListener(new ActionListener()
1437 public void actionPerformed(ActionEvent e)
1439 exportFeatures_actionPerformed(e);
1442 JMenuItem exportAnnotations = new JMenuItem(
1443 MessageManager.getString("label.export_annotations"));
1444 exportAnnotations.addActionListener(new ActionListener()
1447 public void actionPerformed(ActionEvent e)
1449 exportAnnotations_actionPerformed(e);
1452 statusPanel.setLayout(new GridLayout());
1453 JMenuItem showAllSeqs = new JMenuItem(
1454 MessageManager.getString("label.all_sequences"));
1455 showAllSeqs.setToolTipText(
1456 MessageManager.getString("label.toggle_sequence_visibility"));
1457 showAllSeqs.addActionListener(new ActionListener()
1460 public void actionPerformed(ActionEvent e)
1462 showAllSeqs_actionPerformed(e);
1465 JMenuItem showAllColumns = new JMenuItem(
1466 MessageManager.getString("label.all_columns"));
1467 showAllColumns.setToolTipText(
1468 MessageManager.getString("label.toggle_columns_visibility"));
1469 showAllColumns.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 showAllColumns_actionPerformed(e);
1477 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1478 JMenuItem hideSelSequences = new JMenuItem(
1479 MessageManager.getString("label.selected_sequences"));
1480 hideSelSequences.setToolTipText(
1481 MessageManager.getString("label.toggle_sequence_visibility"));
1482 hideSelSequences.addActionListener(new ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 hideSelSequences_actionPerformed(e);
1490 JMenuItem hideSelColumns = new JMenuItem(
1491 MessageManager.getString("label.selected_columns"));
1492 hideSelColumns.setToolTipText(
1493 MessageManager.getString("label.toggle_columns_visibility"));
1494 hideSelColumns.addActionListener(new ActionListener()
1497 public void actionPerformed(ActionEvent e)
1499 hideSelColumns_actionPerformed(e);
1502 JMenuItem hideAllSelection = new JMenuItem(
1503 MessageManager.getString("label.selected_region"));
1504 hideAllSelection.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 hideAllSelection_actionPerformed(e);
1512 // TODO: should be hidden if no selection exists.
1513 JMenuItem hideAllButSelection = new JMenuItem(
1514 MessageManager.getString("label.all_but_selected_region"));
1515 hideAllButSelection.addActionListener(new ActionListener()
1518 public void actionPerformed(ActionEvent e)
1520 hideAllButSelection_actionPerformed(e);
1523 JMenuItem showAllhidden = new JMenuItem(
1524 MessageManager.getString("label.all_sequences_columns"));
1525 showAllhidden.setToolTipText(MessageManager
1526 .getString("label.toggles_visibility_hidden_selected_regions"));
1527 showAllhidden.addActionListener(new ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 showAllhidden_actionPerformed(e);
1535 hiddenMarkers.setText(
1536 MessageManager.getString("action.show_hidden_markers"));
1537 hiddenMarkers.addActionListener(new ActionListener()
1540 public void actionPerformed(ActionEvent e)
1542 hiddenMarkers_actionPerformed(e);
1546 JMenuItem invertColSel = new JMenuItem(
1547 MessageManager.getString("action.invert_column_selection"));
1548 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1549 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1550 | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1552 al = new ActionListener()
1555 public void actionPerformed(ActionEvent e)
1557 invertColSel_actionPerformed(e);
1560 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1562 showComplementMenuItem.setVisible(false);
1563 showComplementMenuItem.addActionListener(new ActionListener()
1566 public void actionPerformed(ActionEvent e)
1568 showComplement_actionPerformed(showComplementMenuItem.getState());
1572 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1575 public void stateChanged(ChangeEvent evt)
1577 JTabbedPane pane = (JTabbedPane) evt.getSource();
1578 int sel = pane.getSelectedIndex();
1579 tabSelectionChanged(sel);
1582 tabbedPane.addMouseListener(new MouseAdapter()
1585 public void mousePressed(MouseEvent e)
1587 if (e.isPopupTrigger()) // Mac
1589 tabbedPane_mousePressed(e);
1594 public void mouseReleased(MouseEvent e)
1596 if (e.isPopupTrigger()) // Windows
1598 tabbedPane_mousePressed(e);
1602 tabbedPane.addFocusListener(new FocusAdapter()
1605 public void focusGained(FocusEvent e)
1607 tabbedPane_focusGained(e);
1611 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1612 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1613 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1614 al = new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 save_actionPerformed(e);
1622 addMenuActionAndAccelerator(keyStroke, save, al);
1624 reload.setEnabled(false);
1625 reload.setText(MessageManager.getString("action.reload"));
1626 reload.addActionListener(new ActionListener()
1629 public void actionPerformed(ActionEvent e)
1631 reload_actionPerformed(e);
1635 JMenuItem newView = new JMenuItem(
1636 MessageManager.getString("action.new_view"));
1637 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1638 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1639 al = new ActionListener()
1642 public void actionPerformed(ActionEvent e)
1644 newView_actionPerformed(e);
1647 addMenuActionAndAccelerator(keyStroke, newView, al);
1649 tabbedPane.setToolTipText("<html><i>"
1650 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1653 formatMenu.setText(MessageManager.getString("action.format"));
1654 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1656 idRightAlign.setText(
1657 MessageManager.getString("label.right_align_sequence_id"));
1658 idRightAlign.addActionListener(new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 idRightAlign_actionPerformed(e);
1667 gatherViews.setEnabled(false);
1668 gatherViews.setText(MessageManager.getString("action.gather_views"));
1669 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1670 al = new ActionListener()
1673 public void actionPerformed(ActionEvent e)
1675 gatherViews_actionPerformed(e);
1678 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1680 expandViews.setEnabled(false);
1681 expandViews.setText(MessageManager.getString("action.expand_views"));
1682 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1683 al = new ActionListener()
1686 public void actionPerformed(ActionEvent e)
1688 expandViews_actionPerformed(e);
1691 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1693 JMenuItem pageSetup = new JMenuItem(
1694 MessageManager.getString("action.page_setup"));
1695 pageSetup.addActionListener(new ActionListener()
1698 public void actionPerformed(ActionEvent e)
1700 pageSetup_actionPerformed(e);
1703 JMenuItem alignmentProperties = new JMenuItem(
1704 MessageManager.getString("label.alignment_props"));
1705 alignmentProperties.addActionListener(new ActionListener()
1708 public void actionPerformed(ActionEvent actionEvent)
1710 alignmentProperties();
1713 JMenuItem selectHighlighted = new JMenuItem(
1714 MessageManager.getString("action.select_highlighted_columns"));
1715 selectHighlighted.setToolTipText(
1716 MessageManager.getString("tooltip.select_highlighted_columns"));
1717 al = new ActionListener()
1720 public void actionPerformed(ActionEvent actionEvent)
1722 selectHighlightedColumns_actionPerformed(actionEvent);
1725 selectHighlighted.addActionListener(al);
1726 JMenu tooltipSettingsMenu = new JMenu(
1727 MessageManager.getString("label.sequence_id_tooltip"));
1728 JMenu autoAnnMenu = new JMenu(
1729 MessageManager.getString("label.autocalculated_annotation"));
1731 JMenu exportImageMenu = new JMenu(
1732 MessageManager.getString("label.export_image"));
1733 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1734 alignFrameMenuBar.add(fileMenu);
1735 alignFrameMenuBar.add(editMenu);
1736 alignFrameMenuBar.add(selectMenu);
1737 alignFrameMenuBar.add(viewMenu);
1738 alignFrameMenuBar.add(annotationsMenu);
1739 alignFrameMenuBar.add(formatMenu);
1740 alignFrameMenuBar.add(colourMenu);
1741 alignFrameMenuBar.add(calculateMenu);
1742 if (!Platform.isJS())
1744 alignFrameMenuBar.add(webService);
1747 fileMenu.add(fetchSequence);
1748 fileMenu.add(addSequenceMenu);
1749 fileMenu.add(reload);
1750 fileMenu.addSeparator();
1751 fileMenu.add(vamsasStore);
1753 fileMenu.add(saveAs);
1754 fileMenu.add(outputTextboxMenu);
1755 fileMenu.add(pageSetup);
1756 fileMenu.add(printMenuItem);
1757 fileMenu.addSeparator();
1758 fileMenu.add(exportImageMenu);
1759 fileMenu.add(exportFeatures);
1760 fileMenu.add(exportAnnotations);
1761 fileMenu.add(loadTreeMenuItem);
1762 fileMenu.add(associatedData);
1763 if (!Platform.isJS())
1765 fileMenu.add(loadVcf);
1767 fileMenu.addSeparator();
1768 fileMenu.add(closeMenuItem);
1770 pasteMenu.add(pasteNew);
1771 pasteMenu.add(pasteThis);
1772 editMenu.add(undoMenuItem);
1773 editMenu.add(redoMenuItem);
1776 editMenu.add(pasteMenu);
1777 editMenu.add(delete);
1778 editMenu.addSeparator();
1779 editMenu.add(remove2LeftMenuItem);
1780 editMenu.add(remove2RightMenuItem);
1781 editMenu.add(removeGappedColumnMenuItem);
1782 editMenu.add(removeAllGapsMenuItem);
1783 editMenu.add(removeRedundancyMenuItem);
1784 editMenu.addSeparator();
1785 // dont add these yet in the CVS build - they cannot be undone!
1786 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1787 // editMenu.add(justifyLeftMenuItem);
1788 // editMenu.add(justifyRightMenuItem);
1789 // editMenu.addSeparator();
1790 editMenu.add(padGapsMenuitem);
1792 showMenu.add(showAllColumns);
1793 showMenu.add(showAllSeqs);
1794 showMenu.add(showAllhidden);
1795 hideMenu.add(hideSelColumns);
1796 hideMenu.add(hideSelSequences);
1797 hideMenu.add(hideAllSelection);
1798 hideMenu.add(hideAllButSelection);
1799 viewMenu.add(newView);
1800 viewMenu.add(expandViews);
1801 viewMenu.add(gatherViews);
1802 viewMenu.addSeparator();
1803 viewMenu.add(showMenu);
1804 viewMenu.add(hideMenu);
1805 viewMenu.add(showComplementMenuItem);
1806 viewMenu.addSeparator();
1807 viewMenu.add(followHighlightMenuItem);
1808 viewMenu.addSeparator();
1809 viewMenu.add(showSeqFeatures);
1810 // viewMenu.add(showSeqFeaturesHeight);
1811 viewMenu.add(openFeatureSettings);
1812 tooltipSettingsMenu.add(showDbRefsMenuitem);
1813 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1814 viewMenu.add(tooltipSettingsMenu);
1815 viewMenu.addSeparator();
1816 viewMenu.add(alignmentProperties);
1817 viewMenu.addSeparator();
1818 viewMenu.add(overviewMenuItem);
1820 annotationsMenu.add(annotationPanelMenuItem);
1821 annotationsMenu.addSeparator();
1822 annotationsMenu.add(showAllAlAnnotations);
1823 annotationsMenu.add(hideAllAlAnnotations);
1824 annotationsMenu.addSeparator();
1825 annotationsMenu.add(showAllSeqAnnotations);
1826 annotationsMenu.add(hideAllSeqAnnotations);
1827 annotationsMenu.add(sortAnnBySequence);
1828 annotationsMenu.add(sortAnnByLabel);
1829 annotationsMenu.addSeparator();
1830 autoAnnMenu.add(showAutoFirst);
1831 autoAnnMenu.add(showAutoLast);
1832 autoAnnMenu.addSeparator();
1833 autoAnnMenu.add(applyAutoAnnotationSettings);
1834 autoAnnMenu.add(showConsensusHistogram);
1835 autoAnnMenu.add(showSequenceLogo);
1836 autoAnnMenu.add(normaliseSequenceLogo);
1837 autoAnnMenu.addSeparator();
1838 autoAnnMenu.add(showGroupConservation);
1839 autoAnnMenu.add(showGroupConsensus);
1840 annotationsMenu.add(autoAnnMenu);
1842 sort.add(sortIDMenuItem);
1843 sort.add(sortLengthMenuItem);
1844 sort.add(sortGroupMenuItem);
1845 sort.add(sortPairwiseMenuItem);
1846 sort.add(sortByTreeMenu);
1847 calculateMenu.add(sort);
1848 calculateMenu.add(calculateTree);
1849 calculateMenu.addSeparator();
1850 calculateMenu.add(pairwiseAlignmentMenuItem);
1851 calculateMenu.addSeparator();
1852 calculateMenu.add(showTranslation);
1853 calculateMenu.add(showReverse);
1854 calculateMenu.add(showReverseComplement);
1855 calculateMenu.add(showProducts);
1856 calculateMenu.add(autoCalculate);
1857 calculateMenu.add(sortByTree);
1858 calculateMenu.addSeparator();
1859 calculateMenu.add(expandAlignment);
1860 calculateMenu.add(extractScores);
1861 if (!Platform.isJS())
1863 calculateMenu.addSeparator();
1864 calculateMenu.add(runGroovy);
1867 webServiceNoServices = new JMenuItem(
1868 MessageManager.getString("label.no_services"));
1869 webService.add(webServiceNoServices);
1870 if (!Platform.isJS())
1872 exportImageMenu.add(htmlMenuItem);
1874 exportImageMenu.add(epsFile);
1875 exportImageMenu.add(createPNG);
1876 if (!Platform.isJS())
1878 exportImageMenu.add(createBioJS);
1879 exportImageMenu.add(createSVG);
1881 addSequenceMenu.add(addFromFile);
1882 addSequenceMenu.add(addFromText);
1883 addSequenceMenu.add(addFromURL);
1884 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1885 statusPanel.add(statusBar, null);
1886 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1888 formatMenu.add(font);
1889 formatMenu.addSeparator();
1890 formatMenu.add(wrapMenuItem);
1891 formatMenu.add(scaleAbove);
1892 formatMenu.add(scaleLeft);
1893 formatMenu.add(scaleRight);
1894 formatMenu.add(seqLimits);
1895 formatMenu.add(idRightAlign);
1896 formatMenu.add(hiddenMarkers);
1897 formatMenu.add(viewBoxesMenuItem);
1898 formatMenu.add(viewTextMenuItem);
1899 formatMenu.add(colourTextMenuItem);
1900 formatMenu.add(renderGapsMenuItem);
1901 formatMenu.add(centreColumnLabelsMenuItem);
1902 formatMenu.add(showNonconservedMenuItem);
1903 selectMenu.add(findMenuItem);
1904 selectMenu.addSeparator();
1905 selectMenu.add(selectAllSequenceMenuItem);
1906 selectMenu.add(deselectAllSequenceMenuItem);
1907 selectMenu.add(invertSequenceMenuItem);
1908 selectMenu.add(invertColSel);
1909 selectMenu.add(createGroup);
1910 selectMenu.add(unGroup);
1911 selectMenu.add(grpsFromSelection);
1912 selectMenu.add(deleteGroups);
1913 selectMenu.add(annotationColumn);
1914 selectMenu.add(selectHighlighted);
1915 // TODO - determine if the listenToViewSelections button is needed : see bug
1917 // selectMenu.addSeparator();
1918 // selectMenu.add(listenToViewSelections);
1921 protected void loadVcf_actionPerformed()
1926 * Constructs the entries on the Colour menu (but does not add them to the
1929 protected void initColourMenu()
1931 applyToAllGroups = new JCheckBoxMenuItem(
1932 MessageManager.getString("label.apply_colour_to_all_groups"));
1933 applyToAllGroups.addActionListener(new ActionListener()
1936 public void actionPerformed(ActionEvent e)
1938 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1942 textColour = new JMenuItem(
1943 MessageManager.getString("label.text_colour"));
1944 textColour.addActionListener(new ActionListener()
1947 public void actionPerformed(ActionEvent e)
1949 textColour_actionPerformed();
1953 conservationMenuItem = new JCheckBoxMenuItem(
1954 MessageManager.getString("action.by_conservation"));
1955 conservationMenuItem.addActionListener(new ActionListener()
1958 public void actionPerformed(ActionEvent e)
1960 conservationMenuItem_actionPerformed(
1961 conservationMenuItem.isSelected());
1965 abovePIDThreshold = new JCheckBoxMenuItem(
1966 MessageManager.getString("label.above_identity_threshold"));
1967 abovePIDThreshold.addActionListener(new ActionListener()
1970 public void actionPerformed(ActionEvent e)
1972 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1975 modifyPID = new JMenuItem(
1976 MessageManager.getString("label.modify_identity_threshold"));
1977 modifyPID.addActionListener(new ActionListener()
1980 public void actionPerformed(ActionEvent e)
1982 modifyPID_actionPerformed();
1985 modifyConservation = new JMenuItem(MessageManager
1986 .getString("label.modify_conservation_threshold"));
1987 modifyConservation.addActionListener(new ActionListener()
1990 public void actionPerformed(ActionEvent e)
1992 modifyConservation_actionPerformed();
1996 annotationColour = new JRadioButtonMenuItem(
1997 MessageManager.getString("action.by_annotation"));
1998 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1999 annotationColour.addActionListener(new ActionListener()
2002 public void actionPerformed(ActionEvent e)
2004 annotationColour_actionPerformed();
2009 protected void selectHighlightedColumns_actionPerformed(
2010 ActionEvent actionEvent)
2012 // TODO Auto-generated method stub
2017 * Generate the reverse sequence (or reverse complement if the flag is true)
2018 * and add it to the alignment
2022 protected void showReverse_actionPerformed(boolean complement)
2027 * Try to run script in a Groovy console, having first ensured that this
2028 * alignframe is set as currentAlignFrame in Desktop
2030 protected void runGroovy_actionPerformed()
2036 * Adds the given action listener and key accelerator to the given menu item.
2037 * Also saves in a lookup table to support lookup of action by key stroke.
2041 * @param actionListener
2043 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2044 JMenuItem menuItem, ActionListener actionListener)
2046 menuItem.setAccelerator(keyStroke);
2047 accelerators.put(keyStroke, menuItem);
2048 menuItem.addActionListener(actionListener);
2052 * Action on clicking sort annotations by type.
2056 protected void sortAnnotations_actionPerformed()
2061 * Action on clicking Show all annotations.
2063 * @param forSequences
2064 * update sequence-related annotations
2065 * @param forAlignment
2066 * update non-sequence-related annotations
2068 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2069 boolean forAlignment)
2071 setAnnotationsVisibility(true, forSequences, forAlignment);
2075 * Action on clicking Hide all annotations.
2077 * @param forSequences
2078 * update sequence-related annotations
2079 * @param forAlignment
2080 * update non-sequence-related annotations
2082 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2083 boolean forAlignment)
2085 setAnnotationsVisibility(false, forSequences, forAlignment);
2089 * Set the visibility of annotations to true or false. Can act on
2090 * sequence-related annotations, or alignment-related, or both.
2093 * @param forSequences
2094 * update sequence-related annotations
2095 * @param forAlignment
2096 * update non-sequence-related annotations
2098 protected void setAnnotationsVisibility(boolean visible,
2099 boolean forSequences, boolean forAlignment)
2104 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2106 // TODO Auto-generated method stub
2110 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2112 // TODO Auto-generated method stub
2116 protected void showAllhidden_actionPerformed(ActionEvent e)
2118 // TODO Auto-generated method stub
2122 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2124 // TODO Auto-generated method stub
2128 protected void hideAllSelection_actionPerformed(ActionEvent e)
2130 // TODO Auto-generated method stub
2134 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2136 // TODO Auto-generated method stub
2140 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2142 // TODO Auto-generated method stub
2146 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2148 // TODO Auto-generated method stub
2152 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2154 // TODO Auto-generated method stub
2158 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2160 // TODO Auto-generated method stub
2164 protected void showGroupConservation_actionPerformed(ActionEvent e)
2166 // TODO Auto-generated method stub
2170 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2172 // TODO Auto-generated method stub
2176 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2178 // TODO Auto-generated method stub
2182 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2184 // TODO Auto-generated method stub
2188 protected void followHighlight_actionPerformed()
2190 // TODO Auto-generated method stub
2194 protected void showNpFeats_actionPerformed(ActionEvent e)
2196 // TODO Auto-generated method stub
2200 protected void showDbRefs_actionPerformed(ActionEvent e)
2202 // TODO Auto-generated method stub
2206 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2210 protected void buildSortByAnnotationScoresMenu()
2214 protected void extractScores_actionPerformed(ActionEvent e)
2218 protected void outputText_actionPerformed(String formatName)
2222 public void addFromFile_actionPerformed(ActionEvent e)
2227 public void addFromText_actionPerformed(ActionEvent e)
2232 public void addFromURL_actionPerformed(ActionEvent e)
2237 public void exportFeatures_actionPerformed(ActionEvent e)
2242 public void exportAnnotations_actionPerformed(ActionEvent e)
2247 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2251 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2256 protected void closeMenuItem_actionPerformed(boolean b)
2260 protected void redoMenuItem_actionPerformed(ActionEvent e)
2264 protected void undoMenuItem_actionPerformed(ActionEvent e)
2268 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2272 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2276 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2280 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2284 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2288 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2292 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2296 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2300 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2304 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2308 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2312 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2316 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2320 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2324 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2328 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2332 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2336 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2340 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2344 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2348 protected void conservationMenuItem_actionPerformed(boolean selected)
2352 protected void printMenuItem_actionPerformed(ActionEvent e)
2356 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2360 protected void findMenuItem_actionPerformed(ActionEvent e)
2364 protected void abovePIDThreshold_actionPerformed(boolean selected)
2368 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2372 protected void deleteGroups_actionPerformed(ActionEvent e)
2376 protected void createGroup_actionPerformed(ActionEvent e)
2380 protected void unGroup_actionPerformed(ActionEvent e)
2384 protected void copy_actionPerformed()
2388 protected void cut_actionPerformed()
2392 protected void delete_actionPerformed()
2396 protected void pasteNew_actionPerformed(ActionEvent e)
2400 protected void pasteThis_actionPerformed(ActionEvent e)
2404 protected void applyToAllGroups_actionPerformed(boolean selected)
2408 public void createPNG(java.io.File f)
2412 protected void font_actionPerformed(ActionEvent e)
2416 protected void seqLimit_actionPerformed(ActionEvent e)
2420 public void seqDBRef_actionPerformed(ActionEvent e)
2425 public void createEPS(java.io.File f)
2429 public void createSVG(java.io.File f)
2434 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2440 * Template method to handle the 'load T-Coffee scores' menu event.
2442 * Subclasses override this method to provide a custom action.
2447 protected void loadScores_actionPerformed(ActionEvent event)
2452 protected void jpred_actionPerformed(ActionEvent e)
2456 protected void scaleAbove_actionPerformed(ActionEvent e)
2460 protected void scaleLeft_actionPerformed(ActionEvent e)
2464 protected void scaleRight_actionPerformed(ActionEvent e)
2468 protected void modifyPID_actionPerformed()
2472 protected void modifyConservation_actionPerformed()
2476 protected void saveAs_actionPerformed()
2480 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2484 public void vamsasStore_actionPerformed(ActionEvent e)
2489 public void vamsasLoad_actionPerformed(ActionEvent e)
2494 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2499 public void featureSettings_actionPerformed(ActionEvent e)
2504 public void fetchSequence_actionPerformed()
2509 public void smoothFont_actionPerformed(ActionEvent e)
2514 public void annotationColour_actionPerformed()
2518 public void annotationColumn_actionPerformed(ActionEvent e)
2522 public void associatedData_actionPerformed(ActionEvent e)
2527 public void autoCalculate_actionPerformed(ActionEvent e)
2532 public void sortByTreeOption_actionPerformed(ActionEvent e)
2537 public void showAllSeqs_actionPerformed(ActionEvent e)
2542 public void showAllColumns_actionPerformed(ActionEvent e)
2547 public void hideSelSequences_actionPerformed(ActionEvent e)
2552 public void hideSelColumns_actionPerformed(ActionEvent e)
2557 public void hiddenMarkers_actionPerformed(ActionEvent e)
2562 public void findPdbId_actionPerformed(ActionEvent e)
2567 public void enterPdbId_actionPerformed(ActionEvent e)
2572 public void pdbFile_actionPerformed(ActionEvent e)
2577 public void invertColSel_actionPerformed(ActionEvent e)
2582 public void tabSelectionChanged(int sel)
2587 public void tabbedPane_mousePressed(MouseEvent e)
2592 public void tabbedPane_focusGained(FocusEvent e)
2597 public void save_actionPerformed(ActionEvent e)
2602 public void reload_actionPerformed(ActionEvent e)
2607 public void newView_actionPerformed(ActionEvent e)
2612 public void textColour_actionPerformed()
2617 public void idRightAlign_actionPerformed(ActionEvent e)
2622 public void expandViews_actionPerformed(ActionEvent e)
2627 public void gatherViews_actionPerformed(ActionEvent e)
2632 public void buildTreeSortMenu()
2637 public void pageSetup_actionPerformed(ActionEvent e)
2642 public void alignmentProperties()
2647 protected void expand_newalign(ActionEvent e)
2649 // TODO Auto-generated method stub
2653 protected boolean isShowAutoCalculatedAbove()
2655 return showAutoCalculatedAbove;
2658 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2660 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2663 protected SequenceAnnotationOrder getAnnotationSortOrder()
2665 return annotationSortOrder;
2668 protected void setAnnotationSortOrder(
2669 SequenceAnnotationOrder annotationSortOrder)
2671 this.annotationSortOrder = annotationSortOrder;
2674 public Map<KeyStroke, JMenuItem> getAccelerators()
2676 return this.accelerators;
2680 * Returns the selected index of the tabbed pane, or -1 if none selected
2681 * (including the case where the tabbed pane has not been made visible).
2685 public int getTabIndex()
2687 return tabbedPane.getSelectedIndex();
2690 public JPanel getStatusPanel()
2696 * Sets a reference to the containing split frame. Also makes the 'toggle
2697 * split view' menu item visible and checked.
2701 public void setSplitFrame(SplitContainerI sf)
2703 this.splitFrame = sf;
2706 this.showComplementMenuItem.setVisible(true);
2707 this.showComplementMenuItem.setState(true);
2711 public SplitContainerI getSplitViewContainer()
2713 return this.splitFrame;
2716 protected void showComplement_actionPerformed(boolean complement)