2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.analysis.GeneticCodeI;
25 import jalview.analysis.GeneticCodes;
26 import jalview.api.SplitContainerI;
27 import jalview.bin.Cache;
28 import jalview.gui.JvSwingUtils;
29 import jalview.gui.Preferences;
30 import jalview.io.FileFormats;
31 import jalview.schemes.ResidueColourScheme;
32 import jalview.util.MessageManager;
33 import jalview.util.Platform;
35 import java.awt.BorderLayout;
36 import java.awt.Color;
37 import java.awt.GridLayout;
38 import java.awt.Toolkit;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.awt.event.FocusAdapter;
42 import java.awt.event.FocusEvent;
43 import java.awt.event.KeyEvent;
44 import java.awt.event.MouseAdapter;
45 import java.awt.event.MouseEvent;
46 import java.util.HashMap;
49 import javax.swing.BorderFactory;
50 import javax.swing.ButtonGroup;
51 import javax.swing.JCheckBoxMenuItem;
52 import javax.swing.JInternalFrame;
53 import javax.swing.JLabel;
54 import javax.swing.JMenu;
55 import javax.swing.JMenuBar;
56 import javax.swing.JMenuItem;
57 import javax.swing.JPanel;
58 import javax.swing.JRadioButtonMenuItem;
59 import javax.swing.JTabbedPane;
60 import javax.swing.KeyStroke;
61 import javax.swing.event.ChangeEvent;
62 import javax.swing.event.MenuEvent;
63 import javax.swing.event.MenuListener;
65 public class GAlignFrame extends JInternalFrame
67 protected JMenuBar alignFrameMenuBar = new JMenuBar();
69 protected JMenuItem closeMenuItem = new JMenuItem();
71 protected JMenu webService = new JMenu();
73 protected JMenuItem webServiceNoServices;
75 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
77 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
79 protected JMenu sortByAnnotScore = new JMenu();
81 protected JLabel statusBar = new JLabel();
83 protected JMenu outputTextboxMenu = new JMenu();
85 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
87 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
89 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
91 protected JMenuItem undoMenuItem = new JMenuItem();
93 protected JMenuItem redoMenuItem = new JMenuItem();
95 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
97 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
99 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
101 JMenuItem copy = new JMenuItem();
103 JMenuItem cut = new JMenuItem();
105 JMenu pasteMenu = new JMenu();
107 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
109 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
111 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
113 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
115 protected JCheckBoxMenuItem applyToAllGroups;
117 protected JMenu colourMenu = new JMenu();
119 protected JMenuItem textColour;
121 protected JCheckBoxMenuItem conservationMenuItem;
123 protected JMenuItem modifyConservation;
125 protected JCheckBoxMenuItem abovePIDThreshold;
127 protected JMenuItem modifyPID;
129 protected JRadioButtonMenuItem annotationColour;
131 protected JMenu sortByTreeMenu = new JMenu();
133 protected JMenu sort = new JMenu();
135 protected JMenuItem calculateTree = new JMenuItem();
137 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
139 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
141 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
143 protected JMenu showTranslation = new JMenu();
145 protected JMenuItem showReverse = new JMenuItem();
147 protected JMenuItem showReverseComplement = new JMenuItem();
149 protected JMenu showProducts = new JMenu();
151 protected JMenuItem runGroovy = new JMenuItem();
153 protected JMenuItem loadVcf;
155 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
157 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
159 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
161 protected JPanel statusPanel = new JPanel();
163 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
165 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
167 protected JMenuItem showAllAlAnnotations = new JMenuItem();
169 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
171 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
173 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
175 protected JTabbedPane tabbedPane = new JTabbedPane();
177 protected JMenuItem reload = new JMenuItem();
179 protected JMenu formatMenu = new JMenu();
181 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
183 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
185 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
187 protected JMenuItem gatherViews = new JMenuItem();
189 protected JMenuItem expandViews = new JMenuItem();
191 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
193 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
203 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
205 private SplitContainerI splitFrame;
207 protected JMenuItem sortAnnBySequence;
209 protected JMenuItem sortAnnByLabel;
211 protected JMenu annotationsMenu;
218 setJMenuBar(alignFrameMenuBar);
220 // dynamically fill save as menu with available formats
221 for (String ff : FileFormats.getInstance().getWritableFormats(true))
223 JMenuItem item = new JMenuItem(ff);
225 item.addActionListener(new ActionListener()
228 public void actionPerformed(ActionEvent e)
230 outputText_actionPerformed(e);
234 outputTextboxMenu.add(item);
236 } catch (Exception e)
238 System.err.println(e.toString());
241 if (!Platform.isAMac())
243 closeMenuItem.setMnemonic('C');
244 outputTextboxMenu.setMnemonic('T');
245 undoMenuItem.setMnemonic('Z');
246 redoMenuItem.setMnemonic('0');
247 copy.setMnemonic('C');
248 cut.setMnemonic('U');
249 pasteMenu.setMnemonic('P');
250 reload.setMnemonic('R');
254 private void jbInit() throws Exception
258 JMenuItem saveAs = new JMenuItem(
259 MessageManager.getString("action.save_as"));
260 ActionListener al = new ActionListener()
263 public void actionPerformed(ActionEvent e)
265 saveAs_actionPerformed(e);
269 // FIXME getDefaultToolkit throws an exception in Headless mode
270 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
271 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
272 | KeyEvent.SHIFT_MASK,
274 addMenuActionAndAccelerator(keyStroke, saveAs, al);
276 closeMenuItem.setText(MessageManager.getString("action.close"));
277 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
278 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
279 al = new ActionListener()
282 public void actionPerformed(ActionEvent e)
284 closeMenuItem_actionPerformed(false);
287 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
289 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
290 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
291 annotationsMenu = new JMenu(
292 MessageManager.getString("action.annotations"));
293 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
294 colourMenu.setText(MessageManager.getString("action.colour"));
295 JMenu calculateMenu = new JMenu(
296 MessageManager.getString("action.calculate"));
297 webService.setText(MessageManager.getString("action.web_service"));
298 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
299 MessageManager.getString("action.select_all"));
300 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
301 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
302 al = new ActionListener()
305 public void actionPerformed(ActionEvent e)
307 selectAllSequenceMenuItem_actionPerformed(e);
310 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
312 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
313 MessageManager.getString("action.deselect_all"));
314 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
315 al = new ActionListener()
318 public void actionPerformed(ActionEvent e)
320 deselectAllSequenceMenuItem_actionPerformed(e);
323 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
325 JMenuItem invertSequenceMenuItem = new JMenuItem(
326 MessageManager.getString("action.invert_sequence_selection"));
327 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
328 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
329 al = new ActionListener()
332 public void actionPerformed(ActionEvent e)
334 invertSequenceMenuItem_actionPerformed(e);
337 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
339 JMenuItem grpsFromSelection = new JMenuItem(
340 MessageManager.getString("action.make_groups_selection"));
341 grpsFromSelection.addActionListener(new ActionListener()
344 public void actionPerformed(ActionEvent e)
346 makeGrpsFromSelection_actionPerformed(e);
349 JMenuItem expandAlignment = new JMenuItem(
350 MessageManager.getString("action.view_flanking_regions"));
351 expandAlignment.setToolTipText(
352 MessageManager.getString("label.view_flanking_regions"));
353 expandAlignment.addActionListener(new ActionListener()
356 public void actionPerformed(ActionEvent e)
361 JMenuItem remove2LeftMenuItem = new JMenuItem(
362 MessageManager.getString("action.remove_left"));
363 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
364 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
365 al = new ActionListener()
368 public void actionPerformed(ActionEvent e)
370 remove2LeftMenuItem_actionPerformed(e);
373 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
375 JMenuItem remove2RightMenuItem = new JMenuItem(
376 MessageManager.getString("action.remove_right"));
377 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
378 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
379 al = new ActionListener()
382 public void actionPerformed(ActionEvent e)
384 remove2RightMenuItem_actionPerformed(e);
387 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
389 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
390 MessageManager.getString("action.remove_empty_columns"));
391 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
392 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
393 al = new ActionListener()
396 public void actionPerformed(ActionEvent e)
398 removeGappedColumnMenuItem_actionPerformed(e);
401 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
403 JMenuItem removeAllGapsMenuItem = new JMenuItem(
404 MessageManager.getString("action.remove_all_gaps"));
405 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
406 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
407 | KeyEvent.SHIFT_MASK,
409 al = new ActionListener()
412 public void actionPerformed(ActionEvent e)
414 removeAllGapsMenuItem_actionPerformed(e);
417 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
419 JMenuItem justifyLeftMenuItem = new JMenuItem(
420 MessageManager.getString("action.left_justify_alignment"));
421 justifyLeftMenuItem.addActionListener(new ActionListener()
424 public void actionPerformed(ActionEvent e)
426 justifyLeftMenuItem_actionPerformed(e);
429 JMenuItem justifyRightMenuItem = new JMenuItem(
430 MessageManager.getString("action.right_justify_alignment"));
431 justifyRightMenuItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent e)
436 justifyRightMenuItem_actionPerformed(e);
439 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
440 viewBoxesMenuItem.setState(true);
441 viewBoxesMenuItem.addActionListener(new ActionListener()
444 public void actionPerformed(ActionEvent e)
446 viewBoxesMenuItem_actionPerformed(e);
449 viewTextMenuItem.setText(MessageManager.getString("action.text"));
450 viewTextMenuItem.setState(true);
451 viewTextMenuItem.addActionListener(new ActionListener()
454 public void actionPerformed(ActionEvent e)
456 viewTextMenuItem_actionPerformed(e);
459 showNonconservedMenuItem
460 .setText(MessageManager.getString("label.show_non_conserved"));
461 showNonconservedMenuItem.setState(false);
462 showNonconservedMenuItem.addActionListener(new ActionListener()
465 public void actionPerformed(ActionEvent e)
467 showUnconservedMenuItem_actionPerformed(e);
470 JMenuItem sortPairwiseMenuItem = new JMenuItem(
471 MessageManager.getString("action.by_pairwise_id"));
472 sortPairwiseMenuItem.addActionListener(new ActionListener()
475 public void actionPerformed(ActionEvent e)
477 sortPairwiseMenuItem_actionPerformed(e);
480 JMenuItem sortIDMenuItem = new JMenuItem(
481 MessageManager.getString("action.by_id"));
482 sortIDMenuItem.addActionListener(new ActionListener()
485 public void actionPerformed(ActionEvent e)
487 sortIDMenuItem_actionPerformed(e);
490 JMenuItem sortLengthMenuItem = new JMenuItem(
491 MessageManager.getString("action.by_length"));
492 sortLengthMenuItem.addActionListener(new ActionListener()
495 public void actionPerformed(ActionEvent e)
497 sortLengthMenuItem_actionPerformed(e);
500 JMenuItem sortGroupMenuItem = new JMenuItem(
501 MessageManager.getString("action.by_group"));
502 sortGroupMenuItem.addActionListener(new ActionListener()
505 public void actionPerformed(ActionEvent e)
507 sortGroupMenuItem_actionPerformed(e);
511 JMenuItem removeRedundancyMenuItem = new JMenuItem(
512 MessageManager.getString("action.remove_redundancy"));
513 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
514 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
515 al = new ActionListener()
518 public void actionPerformed(ActionEvent e)
520 removeRedundancyMenuItem_actionPerformed(e);
523 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
525 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
526 MessageManager.getString("action.pairwise_alignment"));
527 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
530 public void actionPerformed(ActionEvent e)
532 pairwiseAlignmentMenuItem_actionPerformed(e);
536 this.getContentPane().setLayout(new BorderLayout());
537 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
538 statusBar.setBackground(Color.white);
539 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
540 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
541 statusBar.setText(MessageManager.getString("label.status_bar"));
543 .setText(MessageManager.getString("label.out_to_textbox"));
545 annotationPanelMenuItem.setActionCommand("");
546 annotationPanelMenuItem
547 .setText(MessageManager.getString("label.show_annotations"));
548 annotationPanelMenuItem
549 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
550 annotationPanelMenuItem.addActionListener(new ActionListener()
553 public void actionPerformed(ActionEvent e)
555 annotationPanelMenuItem_actionPerformed(e);
558 showAllAlAnnotations.setText(
559 MessageManager.getString("label.show_all_al_annotations"));
560 final boolean isAnnotationPanelShown = annotationPanelMenuItem
562 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
563 showAllAlAnnotations.addActionListener(new ActionListener()
566 public void actionPerformed(ActionEvent e)
568 showAllAnnotations_actionPerformed(false, true);
571 hideAllAlAnnotations.setText(
572 MessageManager.getString("label.hide_all_al_annotations"));
573 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
574 hideAllAlAnnotations.addActionListener(new ActionListener()
577 public void actionPerformed(ActionEvent e)
579 hideAllAnnotations_actionPerformed(false, true);
582 showAllSeqAnnotations.setText(
583 MessageManager.getString("label.show_all_seq_annotations"));
584 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
585 showAllSeqAnnotations.addActionListener(new ActionListener()
588 public void actionPerformed(ActionEvent e)
590 showAllAnnotations_actionPerformed(true, false);
593 hideAllSeqAnnotations.setText(
594 MessageManager.getString("label.hide_all_seq_annotations"));
595 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
596 hideAllSeqAnnotations.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent e)
601 hideAllAnnotations_actionPerformed(true, false);
604 sortAnnBySequence = new JCheckBoxMenuItem(
605 MessageManager.getString("label.sort_annotations_by_sequence"));
606 sortAnnByLabel = new JCheckBoxMenuItem(
607 MessageManager.getString("label.sort_annotations_by_label"));
609 sortAnnBySequence.addActionListener(new ActionListener()
612 public void actionPerformed(ActionEvent e)
614 setAnnotationSortOrder(SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
615 sortAnnotations(false);
618 sortAnnByLabel.addActionListener(new ActionListener()
621 public void actionPerformed(ActionEvent e)
623 setAnnotationSortOrder(SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
624 sortAnnotations(false);
627 colourTextMenuItem = new JCheckBoxMenuItem(
628 MessageManager.getString("label.colour_text"));
629 colourTextMenuItem.addActionListener(new ActionListener()
632 public void actionPerformed(ActionEvent e)
634 colourTextMenuItem_actionPerformed(e);
638 JMenuItem htmlMenuItem = new JMenuItem(
639 MessageManager.getString("label.html"));
640 htmlMenuItem.addActionListener(new ActionListener()
643 public void actionPerformed(ActionEvent e)
645 htmlMenuItem_actionPerformed(e);
649 JMenuItem createBioJS = new JMenuItem(
650 MessageManager.getString("label.biojs_html_export"));
651 createBioJS.addActionListener(new java.awt.event.ActionListener()
654 public void actionPerformed(ActionEvent e)
656 bioJSMenuItem_actionPerformed(e);
660 JMenuItem overviewMenuItem = new JMenuItem(
661 MessageManager.getString("label.overview_window"));
662 overviewMenuItem.addActionListener(new ActionListener()
665 public void actionPerformed(ActionEvent e)
667 overviewMenuItem_actionPerformed(e);
671 undoMenuItem.setEnabled(false);
672 undoMenuItem.setText(MessageManager.getString("action.undo"));
673 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
674 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
675 al = new ActionListener()
678 public void actionPerformed(ActionEvent e)
680 undoMenuItem_actionPerformed(e);
683 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
685 redoMenuItem.setEnabled(false);
686 redoMenuItem.setText(MessageManager.getString("action.redo"));
687 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
688 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
689 al = new ActionListener()
692 public void actionPerformed(ActionEvent e)
694 redoMenuItem_actionPerformed(e);
697 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
699 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
700 wrapMenuItem.addActionListener(new ActionListener()
703 public void actionPerformed(ActionEvent e)
705 wrapMenuItem_actionPerformed(e);
709 JMenuItem printMenuItem = new JMenuItem(
710 MessageManager.getString("action.print"));
711 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
712 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
713 al = new ActionListener()
716 public void actionPerformed(ActionEvent e)
718 printMenuItem_actionPerformed(e);
721 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
724 .setText(MessageManager.getString("action.show_gaps"));
725 renderGapsMenuItem.setState(true);
726 renderGapsMenuItem.addActionListener(new ActionListener()
729 public void actionPerformed(ActionEvent e)
731 renderGapsMenuItem_actionPerformed(e);
735 JMenuItem findMenuItem = new JMenuItem(
736 MessageManager.getString("action.find"));
737 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
738 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
739 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
740 MessageManager.getString("label.find_tip")));
741 al = new ActionListener()
744 public void actionPerformed(ActionEvent e)
746 findMenuItem_actionPerformed(e);
749 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
751 showSeqFeatures.setText(
752 MessageManager.getString("label.show_sequence_features"));
753 showSeqFeatures.addActionListener(new ActionListener()
756 public void actionPerformed(ActionEvent actionEvent)
758 showSeqFeatures_actionPerformed(actionEvent);
762 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
763 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
764 * void actionPerformed(ActionEvent actionEvent) {
765 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
768 .setText(MessageManager.getString("label.show_database_refs"));
769 showDbRefsMenuitem.addActionListener(new ActionListener()
773 public void actionPerformed(ActionEvent e)
775 showDbRefs_actionPerformed(e);
779 showNpFeatsMenuitem.setText(
780 MessageManager.getString("label.show_non_positional_features"));
781 showNpFeatsMenuitem.addActionListener(new ActionListener()
785 public void actionPerformed(ActionEvent e)
787 showNpFeats_actionPerformed(e);
791 showGroupConservation
792 .setText(MessageManager.getString("label.group_conservation"));
793 showGroupConservation.addActionListener(new ActionListener()
797 public void actionPerformed(ActionEvent e)
799 showGroupConservation_actionPerformed(e);
805 .setText(MessageManager.getString("label.group_consensus"));
806 showGroupConsensus.addActionListener(new ActionListener()
810 public void actionPerformed(ActionEvent e)
812 showGroupConsensus_actionPerformed(e);
816 showConsensusHistogram.setText(
817 MessageManager.getString("label.show_consensus_histogram"));
818 showConsensusHistogram.addActionListener(new ActionListener()
822 public void actionPerformed(ActionEvent e)
824 showConsensusHistogram_actionPerformed(e);
829 .setText(MessageManager.getString("label.show_consensus_logo"));
830 showSequenceLogo.addActionListener(new ActionListener()
834 public void actionPerformed(ActionEvent e)
836 showSequenceLogo_actionPerformed(e);
840 normaliseSequenceLogo
841 .setText(MessageManager.getString("label.norm_consensus_logo"));
842 normaliseSequenceLogo.addActionListener(new ActionListener()
846 public void actionPerformed(ActionEvent e)
848 normaliseSequenceLogo_actionPerformed(e);
852 applyAutoAnnotationSettings
853 .setText(MessageManager.getString("label.apply_all_groups"));
854 applyAutoAnnotationSettings.setState(false);
855 applyAutoAnnotationSettings.setVisible(true);
856 applyAutoAnnotationSettings.addActionListener(new ActionListener()
859 public void actionPerformed(ActionEvent e)
861 applyAutoAnnotationSettings_actionPerformed(e);
865 ButtonGroup buttonGroup = new ButtonGroup();
866 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
867 MessageManager.getString("label.show_first"));
868 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
869 MessageManager.getString("label.show_last"));
870 buttonGroup.add(showAutoFirst);
871 buttonGroup.add(showAutoLast);
872 final boolean autoFirst = Cache
873 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
874 showAutoFirst.setSelected(autoFirst);
875 showAutoFirst.addActionListener(new ActionListener()
878 public void actionPerformed(ActionEvent e)
880 if (setShowAutoCalculatedAbove(showAutoFirst.isSelected()))
882 sortAnnotations(true);
886 showAutoLast.setSelected(!showAutoFirst.isSelected());
887 showAutoLast.addActionListener(new ActionListener()
890 public void actionPerformed(ActionEvent e)
892 if (setShowAutoCalculatedAbove(!showAutoLast.isSelected()))
894 sortAnnotations(true);
899 JMenuItem deleteGroups = new JMenuItem(
900 MessageManager.getString("action.undefine_groups"));
901 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
902 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
903 al = new ActionListener()
906 public void actionPerformed(ActionEvent e)
908 deleteGroups_actionPerformed(e);
911 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
913 JMenuItem annotationColumn = new JMenuItem(
914 MessageManager.getString("action.select_by_annotation"));
915 annotationColumn.addActionListener(new ActionListener()
918 public void actionPerformed(ActionEvent e)
920 annotationColumn_actionPerformed(e);
924 JMenuItem createGroup = new JMenuItem(
925 MessageManager.getString("action.create_group"));
926 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
927 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
928 al = new ActionListener()
931 public void actionPerformed(ActionEvent e)
933 createGroup_actionPerformed(e);
936 addMenuActionAndAccelerator(keyStroke, createGroup, al);
938 JMenuItem unGroup = new JMenuItem(
939 MessageManager.getString("action.remove_group"));
940 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
941 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
942 | KeyEvent.SHIFT_MASK,
944 al = new ActionListener()
947 public void actionPerformed(ActionEvent e)
949 unGroup_actionPerformed(e);
952 addMenuActionAndAccelerator(keyStroke, unGroup, al);
954 copy.setText(MessageManager.getString("action.copy"));
955 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
956 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
958 al = new ActionListener()
961 public void actionPerformed(ActionEvent e)
963 copy_actionPerformed(e);
966 addMenuActionAndAccelerator(keyStroke, copy, al);
968 cut.setText(MessageManager.getString("action.cut"));
969 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
970 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
971 al = new ActionListener()
974 public void actionPerformed(ActionEvent e)
976 cut_actionPerformed(e);
979 addMenuActionAndAccelerator(keyStroke, cut, al);
981 JMenuItem delete = new JMenuItem(
982 MessageManager.getString("action.delete"));
983 delete.addActionListener(new ActionListener()
986 public void actionPerformed(ActionEvent e)
988 delete_actionPerformed(e);
992 pasteMenu.setText(MessageManager.getString("action.paste"));
993 JMenuItem pasteNew = new JMenuItem(
994 MessageManager.getString("label.to_new_alignment"));
995 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
996 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
997 | KeyEvent.SHIFT_MASK,
999 al = new ActionListener()
1002 public void actionPerformed(ActionEvent e)
1004 pasteNew_actionPerformed(e);
1007 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1009 JMenuItem pasteThis = new JMenuItem(
1010 MessageManager.getString("label.to_this_alignment"));
1011 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1012 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1013 al = new ActionListener()
1016 public void actionPerformed(ActionEvent e)
1018 pasteThis_actionPerformed(e);
1021 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1023 JMenuItem createPNG = new JMenuItem("PNG");
1024 createPNG.addActionListener(new ActionListener()
1027 public void actionPerformed(ActionEvent e)
1032 createPNG.setActionCommand(
1033 MessageManager.getString("label.save_png_image"));
1035 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1036 font.addActionListener(new ActionListener()
1039 public void actionPerformed(ActionEvent e)
1041 font_actionPerformed(e);
1045 MessageManager.getString("label.show_sequence_limits"));
1046 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1047 seqLimits.addActionListener(new ActionListener()
1050 public void actionPerformed(ActionEvent e)
1052 seqLimit_actionPerformed(e);
1055 JMenuItem epsFile = new JMenuItem("EPS");
1056 epsFile.addActionListener(new ActionListener()
1059 public void actionPerformed(ActionEvent e)
1065 JMenuItem createSVG = new JMenuItem("SVG");
1066 createSVG.addActionListener(new ActionListener()
1069 public void actionPerformed(ActionEvent e)
1075 JMenuItem loadTreeMenuItem = new JMenuItem(
1076 MessageManager.getString("label.load_associated_tree"));
1077 loadTreeMenuItem.setActionCommand(
1078 MessageManager.getString("label.load_tree_for_sequence_set"));
1079 loadTreeMenuItem.addActionListener(new ActionListener()
1082 public void actionPerformed(ActionEvent e)
1084 loadTreeMenuItem_actionPerformed(e);
1088 scaleAbove.setVisible(false);
1089 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1090 scaleAbove.addActionListener(new ActionListener()
1093 public void actionPerformed(ActionEvent e)
1095 scaleAbove_actionPerformed(e);
1098 scaleLeft.setVisible(false);
1099 scaleLeft.setSelected(true);
1100 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1101 scaleLeft.addActionListener(new ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 scaleLeft_actionPerformed(e);
1109 scaleRight.setVisible(false);
1110 scaleRight.setSelected(true);
1111 scaleRight.setText(MessageManager.getString("action.scale_right"));
1112 scaleRight.addActionListener(new ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 scaleRight_actionPerformed(e);
1120 centreColumnLabelsMenuItem.setVisible(true);
1121 centreColumnLabelsMenuItem.setState(false);
1122 centreColumnLabelsMenuItem.setText(
1123 MessageManager.getString("label.centre_column_labels"));
1124 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1127 public void actionPerformed(ActionEvent e)
1129 centreColumnLabels_actionPerformed(e);
1132 followHighlightMenuItem.setVisible(true);
1133 followHighlightMenuItem.setState(true);
1134 followHighlightMenuItem
1135 .setText(MessageManager.getString("label.automatic_scrolling"));
1136 followHighlightMenuItem.addActionListener(new ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 followHighlight_actionPerformed();
1148 .setText(MessageManager.getString("action.by_tree_order"));
1149 sort.setText(MessageManager.getString("action.sort"));
1150 sort.addMenuListener(new MenuListener()
1153 public void menuSelected(MenuEvent e)
1155 buildTreeSortMenu();
1159 public void menuDeselected(MenuEvent e)
1164 public void menuCanceled(MenuEvent e)
1169 .setText(MessageManager.getString("label.sort_by_score"));
1170 sort.add(sortByAnnotScore);
1171 sort.addMenuListener(new javax.swing.event.MenuListener()
1175 public void menuCanceled(MenuEvent e)
1180 public void menuDeselected(MenuEvent e)
1185 public void menuSelected(MenuEvent e)
1187 buildSortByAnnotationScoresMenu();
1190 sortByAnnotScore.setVisible(false);
1193 .setText(MessageManager.getString("action.calculate_tree_pca"));
1195 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1197 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1198 padGapsMenuitem.addActionListener(new ActionListener()
1201 public void actionPerformed(ActionEvent e)
1203 padGapsMenuitem_actionPerformed(e);
1206 JMenuItem vamsasStore = new JMenuItem(
1207 MessageManager.getString("label.vamsas_store"));
1208 vamsasStore.setVisible(false);
1209 vamsasStore.addActionListener(new ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 vamsasStore_actionPerformed(e);
1219 * Translate as cDNA with sub-menu of translation tables
1221 showTranslation.setText(MessageManager
1222 .getString("label.translate_cDNA"));
1223 boolean first = true;
1224 for (final GeneticCodeI table : GeneticCodes.getInstance()
1227 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1228 showTranslation.add(item);
1229 item.addActionListener(new ActionListener()
1232 public void actionPerformed(ActionEvent e)
1234 showTranslation_actionPerformed(table);
1239 showTranslation.addSeparator();
1244 showReverse.setText(MessageManager.getString("label.reverse"));
1245 showReverse.addActionListener(new ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 showReverse_actionPerformed(false);
1253 showReverseComplement
1254 .setText(MessageManager.getString("label.reverse_complement"));
1255 showReverseComplement.addActionListener(new ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 showReverse_actionPerformed(true);
1264 JMenuItem extractScores = new JMenuItem(
1265 MessageManager.getString("label.extract_scores"));
1266 extractScores.addActionListener(new ActionListener()
1269 public void actionPerformed(ActionEvent e)
1271 extractScores_actionPerformed(e);
1274 extractScores.setVisible(true);
1275 // JBPNote: TODO: make gui for regex based score extraction
1277 // for show products actions see AlignFrame.canShowProducts
1278 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1280 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1281 runGroovy.setToolTipText(
1282 MessageManager.getString("label.run_groovy_tip"));
1283 runGroovy.addActionListener(new ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 runGroovy_actionPerformed();
1292 JMenuItem openFeatureSettings = new JMenuItem(
1293 MessageManager.getString("action.feature_settings"));
1294 openFeatureSettings.addActionListener(new ActionListener()
1297 public void actionPerformed(ActionEvent e)
1299 featureSettings_actionPerformed(e);
1302 JMenuItem fetchSequence = new JMenuItem(
1303 MessageManager.getString("label.fetch_sequences"));
1304 fetchSequence.addActionListener(new ActionListener()
1307 public void actionPerformed(ActionEvent e)
1309 fetchSequence_actionPerformed(e);
1313 JMenuItem associatedData = new JMenuItem(
1314 MessageManager.getString("label.load_features_annotations"));
1315 associatedData.addActionListener(new ActionListener()
1318 public void actionPerformed(ActionEvent e)
1320 associatedData_actionPerformed(e);
1323 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1324 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1325 loadVcf.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 loadVcf_actionPerformed();
1333 autoCalculate.setText(
1334 MessageManager.getString("label.autocalculate_consensus"));
1335 autoCalculate.setState(
1336 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1337 autoCalculate.addActionListener(new ActionListener()
1340 public void actionPerformed(ActionEvent e)
1342 autoCalculate_actionPerformed(e);
1346 MessageManager.getString("label.sort_alignment_new_tree"));
1347 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1348 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1350 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1351 sortByTree.addActionListener(new ActionListener()
1354 public void actionPerformed(ActionEvent e)
1356 sortByTreeOption_actionPerformed(e);
1360 listenToViewSelections.setText(
1361 MessageManager.getString("label.listen_for_selections"));
1362 listenToViewSelections
1363 .setToolTipText("<html>" + MessageManager.getString(
1364 "label.selections_mirror_selections_made_same_sequences_other_views"));
1365 listenToViewSelections.setState(false);
1366 listenToViewSelections.addActionListener(new ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 listenToViewSelections_actionPerformed(e);
1375 JMenu addSequenceMenu = new JMenu(
1376 MessageManager.getString("label.add_sequences"));
1377 JMenuItem addFromFile = new JMenuItem(
1378 MessageManager.getString("label.from_file"));
1379 addFromFile.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 addFromFile_actionPerformed(e);
1387 JMenuItem addFromText = new JMenuItem(
1388 MessageManager.getString("label.from_textbox"));
1389 addFromText.addActionListener(new ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 addFromText_actionPerformed(e);
1397 JMenuItem addFromURL = new JMenuItem(
1398 MessageManager.getString("label.from_url"));
1399 addFromURL.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 addFromURL_actionPerformed(e);
1407 JMenuItem exportFeatures = new JMenuItem(
1408 MessageManager.getString("label.export_features"));
1409 exportFeatures.addActionListener(new ActionListener()
1412 public void actionPerformed(ActionEvent e)
1414 exportFeatures_actionPerformed(e);
1417 JMenuItem exportAnnotations = new JMenuItem(
1418 MessageManager.getString("label.export_annotations"));
1419 exportAnnotations.addActionListener(new ActionListener()
1422 public void actionPerformed(ActionEvent e)
1424 exportAnnotations_actionPerformed(e);
1427 statusPanel.setLayout(new GridLayout());
1428 JMenuItem showAllSeqs = new JMenuItem(
1429 MessageManager.getString("label.all_sequences"));
1430 showAllSeqs.setToolTipText(
1431 MessageManager.getString("label.toggle_sequence_visibility"));
1432 showAllSeqs.addActionListener(new ActionListener()
1435 public void actionPerformed(ActionEvent e)
1437 showAllSeqs_actionPerformed(e);
1440 JMenuItem showAllColumns = new JMenuItem(
1441 MessageManager.getString("label.all_columns"));
1442 showAllColumns.setToolTipText(
1443 MessageManager.getString("label.toggle_columns_visibility"));
1444 showAllColumns.addActionListener(new ActionListener()
1447 public void actionPerformed(ActionEvent e)
1449 showAllColumns_actionPerformed(e);
1452 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1453 JMenuItem hideSelSequences = new JMenuItem(
1454 MessageManager.getString("label.selected_sequences"));
1455 hideSelSequences.setToolTipText(
1456 MessageManager.getString("label.toggle_sequence_visibility"));
1457 hideSelSequences.addActionListener(new ActionListener()
1460 public void actionPerformed(ActionEvent e)
1462 hideSelSequences_actionPerformed(e);
1465 JMenuItem hideSelColumns = new JMenuItem(
1466 MessageManager.getString("label.selected_columns"));
1467 hideSelColumns.setToolTipText(
1468 MessageManager.getString("label.toggle_columns_visibility"));
1469 hideSelColumns.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 hideSelColumns_actionPerformed(e);
1477 JMenuItem hideAllSelection = new JMenuItem(
1478 MessageManager.getString("label.selected_region"));
1479 hideAllSelection.addActionListener(new ActionListener()
1482 public void actionPerformed(ActionEvent e)
1484 hideAllSelection_actionPerformed(e);
1487 // TODO: should be hidden if no selection exists.
1488 JMenuItem hideAllButSelection = new JMenuItem(
1489 MessageManager.getString("label.all_but_selected_region"));
1490 hideAllButSelection.addActionListener(new ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 hideAllButSelection_actionPerformed(e);
1498 JMenuItem showAllhidden = new JMenuItem(
1499 MessageManager.getString("label.all_sequences_columns"));
1500 showAllhidden.setToolTipText(MessageManager
1501 .getString("label.toggles_visibility_hidden_selected_regions"));
1502 showAllhidden.addActionListener(new ActionListener()
1505 public void actionPerformed(ActionEvent e)
1507 showAllhidden_actionPerformed(e);
1510 hiddenMarkers.setText(
1511 MessageManager.getString("action.show_hidden_markers"));
1512 hiddenMarkers.addActionListener(new ActionListener()
1515 public void actionPerformed(ActionEvent e)
1517 hiddenMarkers_actionPerformed(e);
1521 JMenuItem invertColSel = new JMenuItem(
1522 MessageManager.getString("action.invert_column_selection"));
1523 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1524 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1525 | KeyEvent.ALT_MASK,
1527 al = new ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 invertColSel_actionPerformed(e);
1535 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1537 showComplementMenuItem.setVisible(false);
1538 showComplementMenuItem.addActionListener(new ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 showComplement_actionPerformed(showComplementMenuItem.getState());
1547 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1550 public void stateChanged(ChangeEvent evt)
1552 JTabbedPane pane = (JTabbedPane) evt.getSource();
1553 int sel = pane.getSelectedIndex();
1554 tabSelectionChanged(sel);
1557 tabbedPane.addMouseListener(new MouseAdapter()
1560 public void mousePressed(MouseEvent e)
1562 if (e.isPopupTrigger()) // Mac
1564 tabbedPane_mousePressed(e);
1569 public void mouseReleased(MouseEvent e)
1571 if (e.isPopupTrigger()) // Windows
1573 tabbedPane_mousePressed(e);
1577 tabbedPane.addFocusListener(new FocusAdapter()
1580 public void focusGained(FocusEvent e)
1582 tabbedPane_focusGained(e);
1586 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1587 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1588 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1589 al = new ActionListener()
1592 public void actionPerformed(ActionEvent e)
1594 save_actionPerformed(e);
1597 addMenuActionAndAccelerator(keyStroke, save, al);
1599 reload.setEnabled(false);
1600 reload.setText(MessageManager.getString("action.reload"));
1601 reload.addActionListener(new ActionListener()
1604 public void actionPerformed(ActionEvent e)
1606 reload_actionPerformed(e);
1610 JMenuItem newView = new JMenuItem(
1611 MessageManager.getString("action.new_view"));
1612 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1613 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1614 al = new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 newView_actionPerformed(e);
1622 addMenuActionAndAccelerator(keyStroke, newView, al);
1624 tabbedPane.setToolTipText("<html><i>"
1625 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1628 formatMenu.setText(MessageManager.getString("action.format"));
1629 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1631 idRightAlign.setText(
1632 MessageManager.getString("label.right_align_sequence_id"));
1633 idRightAlign.addActionListener(new ActionListener()
1636 public void actionPerformed(ActionEvent e)
1638 idRightAlign_actionPerformed(e);
1642 gatherViews.setEnabled(false);
1643 gatherViews.setText(MessageManager.getString("action.gather_views"));
1644 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1645 al = new ActionListener()
1648 public void actionPerformed(ActionEvent e)
1650 gatherViews_actionPerformed(e);
1653 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1655 expandViews.setEnabled(false);
1656 expandViews.setText(MessageManager.getString("action.expand_views"));
1657 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1658 al = new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 expandViews_actionPerformed(e);
1666 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1668 JMenuItem pageSetup = new JMenuItem(
1669 MessageManager.getString("action.page_setup"));
1670 pageSetup.addActionListener(new ActionListener()
1673 public void actionPerformed(ActionEvent e)
1675 pageSetup_actionPerformed(e);
1678 JMenuItem alignmentProperties = new JMenuItem(
1679 MessageManager.getString("label.alignment_props"));
1680 alignmentProperties.addActionListener(new ActionListener()
1683 public void actionPerformed(ActionEvent actionEvent)
1685 alignmentProperties();
1688 JMenuItem selectHighlighted = new JMenuItem(
1689 MessageManager.getString("action.select_highlighted_columns"));
1690 selectHighlighted.setToolTipText(
1691 MessageManager.getString("tooltip.select_highlighted_columns"));
1692 al = new ActionListener()
1695 public void actionPerformed(ActionEvent actionEvent)
1697 selectHighlightedColumns_actionPerformed(actionEvent);
1700 selectHighlighted.addActionListener(al);
1701 JMenu tooltipSettingsMenu = new JMenu(
1702 MessageManager.getString("label.sequence_id_tooltip"));
1703 JMenu autoAnnMenu = new JMenu(
1704 MessageManager.getString("label.autocalculated_annotation"));
1706 JMenu exportImageMenu = new JMenu(
1707 MessageManager.getString("label.export_image"));
1708 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1709 alignFrameMenuBar.add(fileMenu);
1710 alignFrameMenuBar.add(editMenu);
1711 alignFrameMenuBar.add(selectMenu);
1712 alignFrameMenuBar.add(viewMenu);
1713 alignFrameMenuBar.add(annotationsMenu);
1714 alignFrameMenuBar.add(formatMenu);
1715 alignFrameMenuBar.add(colourMenu);
1716 alignFrameMenuBar.add(calculateMenu);
1717 alignFrameMenuBar.add(webService);
1719 fileMenu.add(fetchSequence);
1720 fileMenu.add(addSequenceMenu);
1721 fileMenu.add(reload);
1722 fileMenu.addSeparator();
1723 fileMenu.add(vamsasStore);
1725 fileMenu.add(saveAs);
1726 fileMenu.add(outputTextboxMenu);
1727 fileMenu.add(pageSetup);
1728 fileMenu.add(printMenuItem);
1729 fileMenu.addSeparator();
1730 fileMenu.add(exportImageMenu);
1731 fileMenu.add(exportFeatures);
1732 fileMenu.add(exportAnnotations);
1733 fileMenu.add(loadTreeMenuItem);
1734 fileMenu.add(associatedData);
1735 fileMenu.add(loadVcf);
1736 fileMenu.addSeparator();
1737 fileMenu.add(closeMenuItem);
1739 pasteMenu.add(pasteNew);
1740 pasteMenu.add(pasteThis);
1741 editMenu.add(undoMenuItem);
1742 editMenu.add(redoMenuItem);
1745 editMenu.add(pasteMenu);
1746 editMenu.add(delete);
1747 editMenu.addSeparator();
1748 editMenu.add(remove2LeftMenuItem);
1749 editMenu.add(remove2RightMenuItem);
1750 editMenu.add(removeGappedColumnMenuItem);
1751 editMenu.add(removeAllGapsMenuItem);
1752 editMenu.add(removeRedundancyMenuItem);
1753 editMenu.addSeparator();
1754 // dont add these yet in the CVS build - they cannot be undone!
1755 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1756 // editMenu.add(justifyLeftMenuItem);
1757 // editMenu.add(justifyRightMenuItem);
1758 // editMenu.addSeparator();
1759 editMenu.add(padGapsMenuitem);
1761 showMenu.add(showAllColumns);
1762 showMenu.add(showAllSeqs);
1763 showMenu.add(showAllhidden);
1764 hideMenu.add(hideSelColumns);
1765 hideMenu.add(hideSelSequences);
1766 hideMenu.add(hideAllSelection);
1767 hideMenu.add(hideAllButSelection);
1768 viewMenu.add(newView);
1769 viewMenu.add(expandViews);
1770 viewMenu.add(gatherViews);
1771 viewMenu.addSeparator();
1772 viewMenu.add(showMenu);
1773 viewMenu.add(hideMenu);
1774 viewMenu.add(showComplementMenuItem);
1775 viewMenu.addSeparator();
1776 viewMenu.add(followHighlightMenuItem);
1777 viewMenu.addSeparator();
1778 viewMenu.add(showSeqFeatures);
1779 // viewMenu.add(showSeqFeaturesHeight);
1780 viewMenu.add(openFeatureSettings);
1781 tooltipSettingsMenu.add(showDbRefsMenuitem);
1782 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1783 viewMenu.add(tooltipSettingsMenu);
1784 viewMenu.addSeparator();
1785 viewMenu.add(alignmentProperties);
1786 viewMenu.addSeparator();
1787 viewMenu.add(overviewMenuItem);
1789 annotationsMenu.add(annotationPanelMenuItem);
1790 annotationsMenu.addSeparator();
1791 annotationsMenu.add(showAllAlAnnotations);
1792 annotationsMenu.add(hideAllAlAnnotations);
1793 annotationsMenu.addSeparator();
1794 annotationsMenu.add(showAllSeqAnnotations);
1795 annotationsMenu.add(hideAllSeqAnnotations);
1796 annotationsMenu.add(sortAnnBySequence);
1797 annotationsMenu.add(sortAnnByLabel);
1798 annotationsMenu.addSeparator();
1799 autoAnnMenu.add(showAutoFirst);
1800 autoAnnMenu.add(showAutoLast);
1801 autoAnnMenu.addSeparator();
1802 autoAnnMenu.add(applyAutoAnnotationSettings);
1803 autoAnnMenu.add(showConsensusHistogram);
1804 autoAnnMenu.add(showSequenceLogo);
1805 autoAnnMenu.add(normaliseSequenceLogo);
1806 autoAnnMenu.addSeparator();
1807 autoAnnMenu.add(showGroupConservation);
1808 autoAnnMenu.add(showGroupConsensus);
1809 annotationsMenu.add(autoAnnMenu);
1811 sort.add(sortIDMenuItem);
1812 sort.add(sortLengthMenuItem);
1813 sort.add(sortGroupMenuItem);
1814 sort.add(sortPairwiseMenuItem);
1815 sort.add(sortByTreeMenu);
1816 calculateMenu.add(sort);
1817 calculateMenu.add(calculateTree);
1818 calculateMenu.addSeparator();
1819 calculateMenu.add(pairwiseAlignmentMenuItem);
1820 calculateMenu.addSeparator();
1821 calculateMenu.add(showTranslation);
1822 calculateMenu.add(showReverse);
1823 calculateMenu.add(showReverseComplement);
1824 calculateMenu.add(showProducts);
1825 calculateMenu.add(autoCalculate);
1826 calculateMenu.add(sortByTree);
1827 calculateMenu.addSeparator();
1828 calculateMenu.add(expandAlignment);
1829 calculateMenu.add(extractScores);
1830 calculateMenu.addSeparator();
1831 calculateMenu.add(runGroovy);
1833 webServiceNoServices = new JMenuItem(
1834 MessageManager.getString("label.no_services"));
1835 webService.add(webServiceNoServices);
1836 exportImageMenu.add(htmlMenuItem);
1837 exportImageMenu.add(epsFile);
1838 exportImageMenu.add(createPNG);
1839 exportImageMenu.add(createBioJS);
1840 exportImageMenu.add(createSVG);
1841 addSequenceMenu.add(addFromFile);
1842 addSequenceMenu.add(addFromText);
1843 addSequenceMenu.add(addFromURL);
1844 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1845 statusPanel.add(statusBar, null);
1846 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1848 formatMenu.add(font);
1849 formatMenu.addSeparator();
1850 formatMenu.add(wrapMenuItem);
1851 formatMenu.add(scaleAbove);
1852 formatMenu.add(scaleLeft);
1853 formatMenu.add(scaleRight);
1854 formatMenu.add(seqLimits);
1855 formatMenu.add(idRightAlign);
1856 formatMenu.add(hiddenMarkers);
1857 formatMenu.add(viewBoxesMenuItem);
1858 formatMenu.add(viewTextMenuItem);
1859 formatMenu.add(colourTextMenuItem);
1860 formatMenu.add(renderGapsMenuItem);
1861 formatMenu.add(centreColumnLabelsMenuItem);
1862 formatMenu.add(showNonconservedMenuItem);
1863 selectMenu.add(findMenuItem);
1864 selectMenu.addSeparator();
1865 selectMenu.add(selectAllSequenceMenuItem);
1866 selectMenu.add(deselectAllSequenceMenuItem);
1867 selectMenu.add(invertSequenceMenuItem);
1868 selectMenu.add(invertColSel);
1869 selectMenu.add(createGroup);
1870 selectMenu.add(unGroup);
1871 selectMenu.add(grpsFromSelection);
1872 selectMenu.add(deleteGroups);
1873 selectMenu.add(annotationColumn);
1874 selectMenu.add(selectHighlighted);
1875 // TODO - determine if the listenToViewSelections button is needed : see bug
1877 // selectMenu.addSeparator();
1878 // selectMenu.add(listenToViewSelections);
1881 protected void loadVcf_actionPerformed()
1886 * Constructs the entries on the Colour menu (but does not add them to the
1889 protected void initColourMenu()
1891 applyToAllGroups = new JCheckBoxMenuItem(
1892 MessageManager.getString("label.apply_colour_to_all_groups"));
1893 applyToAllGroups.addActionListener(new ActionListener()
1896 public void actionPerformed(ActionEvent e)
1898 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1902 textColour = new JMenuItem(
1903 MessageManager.getString("label.text_colour"));
1904 textColour.addActionListener(new ActionListener()
1907 public void actionPerformed(ActionEvent e)
1909 textColour_actionPerformed();
1913 conservationMenuItem = new JCheckBoxMenuItem(
1914 MessageManager.getString("action.by_conservation"));
1915 conservationMenuItem.addActionListener(new ActionListener()
1918 public void actionPerformed(ActionEvent e)
1920 conservationMenuItem_actionPerformed(
1921 conservationMenuItem.isSelected());
1925 abovePIDThreshold = new JCheckBoxMenuItem(
1926 MessageManager.getString("label.above_identity_threshold"));
1927 abovePIDThreshold.addActionListener(new ActionListener()
1930 public void actionPerformed(ActionEvent e)
1932 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1935 modifyPID = new JMenuItem(
1936 MessageManager.getString("label.modify_identity_threshold"));
1937 modifyPID.addActionListener(new ActionListener()
1940 public void actionPerformed(ActionEvent e)
1942 modifyPID_actionPerformed();
1945 modifyConservation = new JMenuItem(MessageManager
1946 .getString("label.modify_conservation_threshold"));
1947 modifyConservation.addActionListener(new ActionListener()
1950 public void actionPerformed(ActionEvent e)
1952 modifyConservation_actionPerformed();
1956 annotationColour = new JRadioButtonMenuItem(
1957 MessageManager.getString("action.by_annotation"));
1958 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1959 annotationColour.addActionListener(new ActionListener()
1962 public void actionPerformed(ActionEvent e)
1964 annotationColour_actionPerformed();
1969 protected void selectHighlightedColumns_actionPerformed(
1970 ActionEvent actionEvent)
1972 // TODO Auto-generated method stub
1977 * Generate the reverse sequence (or reverse complement if the flag is true)
1978 * and add it to the alignment
1982 protected void showReverse_actionPerformed(boolean complement)
1987 * Try to run script in a Groovy console, having first ensured that this
1988 * alignframe is set as currentAlignFrame in Desktop
1990 protected void runGroovy_actionPerformed()
1996 * Adds the given action listener and key accelerator to the given menu item.
1997 * Also saves in a lookup table to support lookup of action by key stroke.
2001 * @param actionListener
2003 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2004 JMenuItem menuItem, ActionListener actionListener)
2006 menuItem.setAccelerator(keyStroke);
2007 accelerators.put(keyStroke, menuItem);
2008 menuItem.addActionListener(actionListener);
2012 * Action on clicking sort annotations by type, or change position of
2013 * autocalculated annotation
2015 * @param autoCalcOnly
2017 protected void sortAnnotations(boolean autoCalcOnly)
2022 * Action on clicking Show all annotations.
2024 * @param forSequences
2025 * update sequence-related annotations
2026 * @param forAlignment
2027 * update non-sequence-related annotations
2029 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2030 boolean forAlignment)
2032 setAnnotationsVisibility(true, forSequences, forAlignment);
2036 * Action on clicking Hide all annotations.
2038 * @param forSequences
2039 * update sequence-related annotations
2040 * @param forAlignment
2041 * update non-sequence-related annotations
2043 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2044 boolean forAlignment)
2046 setAnnotationsVisibility(false, forSequences, forAlignment);
2050 * Set the visibility of annotations to true or false. Can act on
2051 * sequence-related annotations, or alignment-related, or both.
2054 * @param forSequences
2055 * update sequence-related annotations
2056 * @param forAlignment
2057 * update non-sequence-related annotations
2059 protected void setAnnotationsVisibility(boolean visible,
2060 boolean forSequences, boolean forAlignment)
2065 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2067 // TODO Auto-generated method stub
2071 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2073 // TODO Auto-generated method stub
2077 protected void showAllhidden_actionPerformed(ActionEvent e)
2079 // TODO Auto-generated method stub
2083 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2085 // TODO Auto-generated method stub
2089 protected void hideAllSelection_actionPerformed(ActionEvent e)
2091 // TODO Auto-generated method stub
2095 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2097 // TODO Auto-generated method stub
2101 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2103 // TODO Auto-generated method stub
2107 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2109 // TODO Auto-generated method stub
2113 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2115 // TODO Auto-generated method stub
2119 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2121 // TODO Auto-generated method stub
2125 protected void showGroupConservation_actionPerformed(ActionEvent e)
2127 // TODO Auto-generated method stub
2131 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2133 // TODO Auto-generated method stub
2137 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2139 // TODO Auto-generated method stub
2143 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2145 // TODO Auto-generated method stub
2149 protected void followHighlight_actionPerformed()
2151 // TODO Auto-generated method stub
2155 protected void showNpFeats_actionPerformed(ActionEvent e)
2157 // TODO Auto-generated method stub
2161 protected void showDbRefs_actionPerformed(ActionEvent e)
2163 // TODO Auto-generated method stub
2167 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2171 protected void buildSortByAnnotationScoresMenu()
2175 protected void extractScores_actionPerformed(ActionEvent e)
2179 protected void outputText_actionPerformed(ActionEvent e)
2183 public void addFromFile_actionPerformed(ActionEvent e)
2188 public void addFromText_actionPerformed(ActionEvent e)
2193 public void addFromURL_actionPerformed(ActionEvent e)
2198 public void exportFeatures_actionPerformed(ActionEvent e)
2203 public void exportAnnotations_actionPerformed(ActionEvent e)
2208 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2212 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2217 protected void closeMenuItem_actionPerformed(boolean b)
2221 protected void redoMenuItem_actionPerformed(ActionEvent e)
2225 protected void undoMenuItem_actionPerformed(ActionEvent e)
2229 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2233 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2237 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2241 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2245 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2249 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2253 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2257 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2261 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2265 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2269 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2273 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2277 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2281 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2285 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2289 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2293 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2297 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2301 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2305 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2309 protected void conservationMenuItem_actionPerformed(boolean selected)
2313 protected void printMenuItem_actionPerformed(ActionEvent e)
2317 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2321 protected void findMenuItem_actionPerformed(ActionEvent e)
2325 protected void abovePIDThreshold_actionPerformed(boolean selected)
2329 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2333 protected void deleteGroups_actionPerformed(ActionEvent e)
2337 protected void createGroup_actionPerformed(ActionEvent e)
2341 protected void unGroup_actionPerformed(ActionEvent e)
2345 protected void copy_actionPerformed(ActionEvent e)
2349 protected void cut_actionPerformed(ActionEvent e)
2353 protected void delete_actionPerformed(ActionEvent e)
2357 protected void pasteNew_actionPerformed(ActionEvent e)
2361 protected void pasteThis_actionPerformed(ActionEvent e)
2365 protected void applyToAllGroups_actionPerformed(boolean selected)
2369 public void createPNG(java.io.File f)
2373 protected void font_actionPerformed(ActionEvent e)
2377 protected void seqLimit_actionPerformed(ActionEvent e)
2381 public void seqDBRef_actionPerformed(ActionEvent e)
2386 public void createEPS(java.io.File f)
2390 public void createSVG(java.io.File f)
2395 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2401 * Template method to handle the 'load T-Coffee scores' menu event.
2403 * Subclasses override this method to provide a custom action.
2408 protected void loadScores_actionPerformed(ActionEvent event)
2413 protected void jpred_actionPerformed(ActionEvent e)
2417 protected void scaleAbove_actionPerformed(ActionEvent e)
2421 protected void scaleLeft_actionPerformed(ActionEvent e)
2425 protected void scaleRight_actionPerformed(ActionEvent e)
2429 protected void modifyPID_actionPerformed()
2433 protected void modifyConservation_actionPerformed()
2437 protected void saveAs_actionPerformed(ActionEvent e)
2441 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2445 public void vamsasStore_actionPerformed(ActionEvent e)
2450 public void vamsasLoad_actionPerformed(ActionEvent e)
2455 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2460 public void featureSettings_actionPerformed(ActionEvent e)
2465 public void fetchSequence_actionPerformed(ActionEvent e)
2470 public void smoothFont_actionPerformed(ActionEvent e)
2475 public void annotationColour_actionPerformed()
2479 public void annotationColumn_actionPerformed(ActionEvent e)
2483 public void associatedData_actionPerformed(ActionEvent e)
2488 public void autoCalculate_actionPerformed(ActionEvent e)
2493 public void sortByTreeOption_actionPerformed(ActionEvent e)
2498 public void showAllSeqs_actionPerformed(ActionEvent e)
2503 public void showAllColumns_actionPerformed(ActionEvent e)
2508 public void hideSelSequences_actionPerformed(ActionEvent e)
2513 public void hideSelColumns_actionPerformed(ActionEvent e)
2518 public void hiddenMarkers_actionPerformed(ActionEvent e)
2523 public void findPdbId_actionPerformed(ActionEvent e)
2528 public void enterPdbId_actionPerformed(ActionEvent e)
2533 public void pdbFile_actionPerformed(ActionEvent e)
2538 public void invertColSel_actionPerformed(ActionEvent e)
2543 public void tabSelectionChanged(int sel)
2548 public void tabbedPane_mousePressed(MouseEvent e)
2553 public void tabbedPane_focusGained(FocusEvent e)
2558 public void save_actionPerformed(ActionEvent e)
2563 public void reload_actionPerformed(ActionEvent e)
2568 public void newView_actionPerformed(ActionEvent e)
2573 public void textColour_actionPerformed()
2578 public void idRightAlign_actionPerformed(ActionEvent e)
2583 public void expandViews_actionPerformed(ActionEvent e)
2588 public void gatherViews_actionPerformed(ActionEvent e)
2593 public void buildTreeSortMenu()
2598 public void pageSetup_actionPerformed(ActionEvent e)
2603 public void alignmentProperties()
2608 protected void expand_newalign(ActionEvent e)
2610 // TODO Auto-generated method stub
2615 * Sets the value of the flag for 'show autocalculated annotations above other
2616 * annotations'. Answers true if the value changed, else false.
2618 * @param showAutoCalculatedAbove
2621 protected boolean setShowAutoCalculatedAbove(
2622 boolean showAutoCalculatedAbove)
2627 public void setAnnotationSortOrder(
2628 SequenceAnnotationOrder annotationSortOrder)
2632 public Map<KeyStroke, JMenuItem> getAccelerators()
2634 return this.accelerators;
2638 * Returns the selected index of the tabbed pane, or -1 if none selected
2639 * (including the case where the tabbed pane has not been made visible).
2643 public int getTabIndex()
2645 return tabbedPane.getSelectedIndex();
2648 public JPanel getStatusPanel()
2654 * Sets a reference to the containing split frame. Also makes the 'toggle
2655 * split view' menu item visible and checked.
2659 public void setSplitFrame(SplitContainerI sf)
2661 this.splitFrame = sf;
2664 this.showComplementMenuItem.setVisible(true);
2665 this.showComplementMenuItem.setState(true);
2669 public SplitContainerI getSplitViewContainer()
2671 return this.splitFrame;
2674 protected void showComplement_actionPerformed(boolean complement)