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.hmmer.HmmerCommand;
31 import jalview.io.FileFormatException;
32 import jalview.io.FileFormats;
33 import jalview.schemes.ResidueColourScheme;
34 import jalview.util.MessageManager;
35 import jalview.util.Platform;
37 import java.awt.BorderLayout;
38 import java.awt.Color;
39 import java.awt.GridLayout;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.event.FocusAdapter;
43 import java.awt.event.FocusEvent;
44 import java.awt.event.KeyEvent;
45 import java.awt.event.MouseAdapter;
46 import java.awt.event.MouseEvent;
47 import java.io.IOException;
48 import java.util.HashMap;
51 import javax.swing.BorderFactory;
52 import javax.swing.ButtonGroup;
53 import javax.swing.JCheckBoxMenuItem;
54 import javax.swing.JInternalFrame;
55 import javax.swing.JLabel;
56 import javax.swing.JMenu;
57 import javax.swing.JMenuBar;
58 import javax.swing.JMenuItem;
59 import javax.swing.JPanel;
60 import javax.swing.JRadioButtonMenuItem;
61 import javax.swing.JTabbedPane;
62 import javax.swing.KeyStroke;
63 import javax.swing.event.ChangeEvent;
64 import javax.swing.event.MenuEvent;
65 import javax.swing.event.MenuListener;
67 public class GAlignFrame extends JInternalFrame
69 protected JMenuBar alignFrameMenuBar = new JMenuBar();
71 protected JMenuItem closeMenuItem = new JMenuItem();
73 protected JMenu webService = new JMenu();
75 protected JMenu hmmerMenu = new JMenu();
77 protected JMenuItem webServiceNoServices;
79 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
81 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
83 protected JMenu sortByAnnotScore = new JMenu();
85 protected JLabel statusBar = new JLabel();
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 showInformationHistogram = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
209 protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
211 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
213 private SequenceAnnotationOrder annotationSortOrder;
215 private boolean showAutoCalculatedAbove = false;
217 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
219 private SplitContainerI splitFrame;
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);
242 outputTextboxMenu.add(item);
244 } catch (Exception e)
246 System.err.println(e.toString());
249 if (!Platform.isAMac())
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(e);
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"));
309 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
310 MessageManager.getString("action.select_all"));
311 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
312 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
313 al = new ActionListener()
316 public void actionPerformed(ActionEvent e)
318 selectAllSequenceMenuItem_actionPerformed(e);
321 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
323 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
324 MessageManager.getString("action.deselect_all"));
325 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
326 al = new ActionListener()
329 public void actionPerformed(ActionEvent e)
331 deselectAllSequenceMenuItem_actionPerformed(e);
334 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
336 JMenuItem invertSequenceMenuItem = new JMenuItem(
337 MessageManager.getString("action.invert_sequence_selection"));
338 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
339 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
340 al = new ActionListener()
343 public void actionPerformed(ActionEvent e)
345 invertSequenceMenuItem_actionPerformed(e);
348 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
350 JMenuItem grpsFromSelection = new JMenuItem(
351 MessageManager.getString("action.make_groups_selection"));
352 grpsFromSelection.addActionListener(new ActionListener()
355 public void actionPerformed(ActionEvent e)
357 makeGrpsFromSelection_actionPerformed(e);
360 JMenuItem expandAlignment = new JMenuItem(
361 MessageManager.getString("action.view_flanking_regions"));
362 expandAlignment.setToolTipText(
363 MessageManager.getString("label.view_flanking_regions"));
364 expandAlignment.addActionListener(new ActionListener()
367 public void actionPerformed(ActionEvent e)
372 JMenuItem remove2LeftMenuItem = new JMenuItem(
373 MessageManager.getString("action.remove_left"));
374 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
375 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
376 al = new ActionListener()
379 public void actionPerformed(ActionEvent e)
381 remove2LeftMenuItem_actionPerformed(e);
384 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
386 JMenuItem remove2RightMenuItem = new JMenuItem(
387 MessageManager.getString("action.remove_right"));
388 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
389 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
390 al = new ActionListener()
393 public void actionPerformed(ActionEvent e)
395 remove2RightMenuItem_actionPerformed(e);
398 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
400 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
401 MessageManager.getString("action.remove_empty_columns"));
402 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
403 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
404 al = new ActionListener()
407 public void actionPerformed(ActionEvent e)
409 removeGappedColumnMenuItem_actionPerformed(e);
412 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
414 JMenuItem removeAllGapsMenuItem = new JMenuItem(
415 MessageManager.getString("action.remove_all_gaps"));
416 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
417 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
418 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
420 al = new ActionListener()
423 public void actionPerformed(ActionEvent e)
425 removeAllGapsMenuItem_actionPerformed(e);
428 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
430 JMenuItem justifyLeftMenuItem = new JMenuItem(
431 MessageManager.getString("action.left_justify_alignment"));
432 justifyLeftMenuItem.addActionListener(new ActionListener()
435 public void actionPerformed(ActionEvent e)
437 justifyLeftMenuItem_actionPerformed(e);
440 JMenuItem justifyRightMenuItem = new JMenuItem(
441 MessageManager.getString("action.right_justify_alignment"));
442 justifyRightMenuItem.addActionListener(new ActionListener()
445 public void actionPerformed(ActionEvent e)
447 justifyRightMenuItem_actionPerformed(e);
450 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
451 viewBoxesMenuItem.setState(true);
452 viewBoxesMenuItem.addActionListener(new ActionListener()
455 public void actionPerformed(ActionEvent e)
457 viewBoxesMenuItem_actionPerformed(e);
460 viewTextMenuItem.setText(MessageManager.getString("action.text"));
461 viewTextMenuItem.setState(true);
462 viewTextMenuItem.addActionListener(new ActionListener()
465 public void actionPerformed(ActionEvent e)
467 viewTextMenuItem_actionPerformed(e);
470 showNonconservedMenuItem
471 .setText(MessageManager.getString("label.show_non_conserved"));
472 showNonconservedMenuItem.setState(false);
473 showNonconservedMenuItem.addActionListener(new ActionListener()
476 public void actionPerformed(ActionEvent e)
478 showUnconservedMenuItem_actionPerformed(e);
481 JMenuItem sortPairwiseMenuItem = new JMenuItem(
482 MessageManager.getString("action.by_pairwise_id"));
483 sortPairwiseMenuItem.addActionListener(new ActionListener()
486 public void actionPerformed(ActionEvent e)
488 sortPairwiseMenuItem_actionPerformed(e);
491 JMenuItem sortIDMenuItem = new JMenuItem(
492 MessageManager.getString("action.by_id"));
493 sortIDMenuItem.addActionListener(new ActionListener()
496 public void actionPerformed(ActionEvent e)
498 sortIDMenuItem_actionPerformed(e);
501 JMenuItem sortLengthMenuItem = new JMenuItem(
502 MessageManager.getString("action.by_length"));
503 sortLengthMenuItem.addActionListener(new ActionListener()
506 public void actionPerformed(ActionEvent e)
508 sortLengthMenuItem_actionPerformed(e);
511 JMenuItem sortGroupMenuItem = new JMenuItem(
512 MessageManager.getString("action.by_group"));
513 sortGroupMenuItem.addActionListener(new ActionListener()
516 public void actionPerformed(ActionEvent e)
518 sortGroupMenuItem_actionPerformed(e);
521 JMenuItem sortEValueMenuItem = new JMenuItem(
522 MessageManager.getString("action.by_evalue"));
523 sortEValueMenuItem.addActionListener(new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 sortEValueMenuItem_actionPerformed(e);
531 JMenuItem sortBitScoreMenuItem = new JMenuItem(
532 MessageManager.getString("action.by_bit_score"));
533 sortBitScoreMenuItem.addActionListener(new ActionListener()
536 public void actionPerformed(ActionEvent e)
538 sortBitScoreMenuItem_actionPerformed(e);
542 JMenuItem removeRedundancyMenuItem = new JMenuItem(
543 MessageManager.getString("action.remove_redundancy"));
544 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
545 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
546 al = new ActionListener()
549 public void actionPerformed(ActionEvent e)
551 removeRedundancyMenuItem_actionPerformed(e);
554 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
556 JMenuItem filterByEValue = new JMenuItem(
557 MessageManager.getString("action.filter_by_evalue"));
558 filterByEValue.addActionListener(new ActionListener()
561 public void actionPerformed(ActionEvent e)
563 filterByEValue_actionPerformed();
568 JMenuItem filterByScore = new JMenuItem(
569 MessageManager.getString("action.filter_by_score"));
570 filterByScore.addActionListener(new ActionListener()
573 public void actionPerformed(ActionEvent e)
575 filterByScore_actionPerformed();
580 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
581 MessageManager.getString("action.pairwise_alignment"));
582 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
585 public void actionPerformed(ActionEvent e)
587 pairwiseAlignmentMenuItem_actionPerformed(e);
591 this.getContentPane().setLayout(new BorderLayout());
592 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
593 statusBar.setBackground(Color.white);
594 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
595 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
596 statusBar.setText(MessageManager.getString("label.status_bar"));
599 .setText(MessageManager.getString("label.out_to_textbox"));
602 annotationPanelMenuItem.setActionCommand("");
603 annotationPanelMenuItem
604 .setText(MessageManager.getString("label.show_annotations"));
605 annotationPanelMenuItem
606 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
607 annotationPanelMenuItem.addActionListener(new ActionListener()
610 public void actionPerformed(ActionEvent e)
612 annotationPanelMenuItem_actionPerformed(e);
615 showAllAlAnnotations.setText(
616 MessageManager.getString("label.show_all_al_annotations"));
617 final boolean isAnnotationPanelShown = annotationPanelMenuItem
619 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
620 showAllAlAnnotations.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent e)
625 showAllAnnotations_actionPerformed(false, true);
628 hideAllAlAnnotations.setText(
629 MessageManager.getString("label.hide_all_al_annotations"));
630 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
631 hideAllAlAnnotations.addActionListener(new ActionListener()
634 public void actionPerformed(ActionEvent e)
636 hideAllAnnotations_actionPerformed(false, true);
639 showAllSeqAnnotations.setText(
640 MessageManager.getString("label.show_all_seq_annotations"));
641 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
642 showAllSeqAnnotations.addActionListener(new ActionListener()
645 public void actionPerformed(ActionEvent e)
647 showAllAnnotations_actionPerformed(true, false);
650 hideAllSeqAnnotations.setText(
651 MessageManager.getString("label.hide_all_seq_annotations"));
652 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
653 hideAllSeqAnnotations.addActionListener(new ActionListener()
656 public void actionPerformed(ActionEvent e)
658 hideAllAnnotations_actionPerformed(true, false);
661 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
662 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
663 SequenceAnnotationOrder.NONE.name()));
664 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
665 MessageManager.getString("label.sort_annotations_by_sequence"));
666 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
667 MessageManager.getString("label.sort_annotations_by_label"));
670 sortAnnBySequence.setSelected(
671 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
672 sortAnnBySequence.addActionListener(new ActionListener()
675 public void actionPerformed(ActionEvent e)
677 boolean newState = sortAnnBySequence.getState();
678 sortAnnByLabel.setSelected(false);
679 setAnnotationSortOrder(
680 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
681 : SequenceAnnotationOrder.NONE);
682 sortAnnotations_actionPerformed();
685 sortAnnByLabel.setSelected(
686 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
687 sortAnnByLabel.addActionListener(new ActionListener()
690 public void actionPerformed(ActionEvent e)
692 boolean newState = sortAnnByLabel.getState();
693 sortAnnBySequence.setSelected(false);
694 setAnnotationSortOrder(
695 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
696 : SequenceAnnotationOrder.NONE);
697 sortAnnotations_actionPerformed();
700 colourTextMenuItem = new JCheckBoxMenuItem(
701 MessageManager.getString("label.colour_text"));
702 colourTextMenuItem.addActionListener(new ActionListener()
705 public void actionPerformed(ActionEvent e)
707 colourTextMenuItem_actionPerformed(e);
711 JMenuItem htmlMenuItem = new JMenuItem(
712 MessageManager.getString("label.html"));
713 htmlMenuItem.addActionListener(new ActionListener()
716 public void actionPerformed(ActionEvent e)
718 htmlMenuItem_actionPerformed(e);
722 JMenuItem createBioJS = new JMenuItem(
723 MessageManager.getString("label.biojs_html_export"));
724 createBioJS.addActionListener(new java.awt.event.ActionListener()
727 public void actionPerformed(ActionEvent e)
729 bioJSMenuItem_actionPerformed(e);
733 JMenuItem overviewMenuItem = new JMenuItem(
734 MessageManager.getString("label.overview_window"));
735 overviewMenuItem.addActionListener(new ActionListener()
738 public void actionPerformed(ActionEvent e)
740 overviewMenuItem_actionPerformed(e);
744 undoMenuItem.setEnabled(false);
745 undoMenuItem.setText(MessageManager.getString("action.undo"));
746 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
747 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
748 al = new ActionListener()
751 public void actionPerformed(ActionEvent e)
753 undoMenuItem_actionPerformed(e);
756 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
758 redoMenuItem.setEnabled(false);
759 redoMenuItem.setText(MessageManager.getString("action.redo"));
760 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
761 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
762 al = new ActionListener()
765 public void actionPerformed(ActionEvent e)
767 redoMenuItem_actionPerformed(e);
770 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
772 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
773 wrapMenuItem.addActionListener(new ActionListener()
776 public void actionPerformed(ActionEvent e)
778 wrapMenuItem_actionPerformed(e);
782 JMenuItem printMenuItem = new JMenuItem(
783 MessageManager.getString("action.print"));
784 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
785 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
786 al = new ActionListener()
789 public void actionPerformed(ActionEvent e)
791 printMenuItem_actionPerformed(e);
794 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
797 .setText(MessageManager.getString("action.show_gaps"));
798 renderGapsMenuItem.setState(true);
799 renderGapsMenuItem.addActionListener(new ActionListener()
802 public void actionPerformed(ActionEvent e)
804 renderGapsMenuItem_actionPerformed(e);
808 JMenuItem findMenuItem = new JMenuItem(
809 MessageManager.getString("action.find"));
810 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
811 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
812 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
813 MessageManager.getString("label.find_tip")));
814 al = new ActionListener()
817 public void actionPerformed(ActionEvent e)
819 findMenuItem_actionPerformed(e);
822 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
824 showSeqFeatures.setText(
825 MessageManager.getString("label.show_sequence_features"));
827 showSeqFeatures.addActionListener(new ActionListener()
830 public void actionPerformed(ActionEvent actionEvent)
832 showSeqFeatures_actionPerformed(actionEvent);
836 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
837 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
838 * void actionPerformed(ActionEvent actionEvent) {
839 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
842 .setText(MessageManager.getString("label.show_database_refs"));
843 showDbRefsMenuitem.addActionListener(new ActionListener()
847 public void actionPerformed(ActionEvent e)
849 showDbRefs_actionPerformed(e);
853 showNpFeatsMenuitem.setText(
854 MessageManager.getString("label.show_non_positional_features"));
855 showNpFeatsMenuitem.addActionListener(new ActionListener()
859 public void actionPerformed(ActionEvent e)
861 showNpFeats_actionPerformed(e);
865 showGroupConservation
866 .setText(MessageManager.getString("label.group_conservation"));
867 showGroupConservation.addActionListener(new ActionListener()
871 public void actionPerformed(ActionEvent e)
873 showGroupConservation_actionPerformed(e);
879 .setText(MessageManager.getString("label.group_consensus"));
880 showGroupConsensus.addActionListener(new ActionListener()
884 public void actionPerformed(ActionEvent e)
886 showGroupConsensus_actionPerformed(e);
890 showConsensusHistogram.setText(
891 MessageManager.getString("label.show_consensus_histogram"));
892 showConsensusHistogram.addActionListener(new ActionListener()
896 public void actionPerformed(ActionEvent e)
898 showConsensusHistogram_actionPerformed(e);
903 .setText(MessageManager.getString("label.show_consensus_logo"));
904 showSequenceLogo.addActionListener(new ActionListener()
908 public void actionPerformed(ActionEvent e)
910 showSequenceLogo_actionPerformed(e);
914 normaliseSequenceLogo
915 .setText(MessageManager.getString("label.norm_consensus_logo"));
916 normaliseSequenceLogo.addActionListener(new ActionListener()
920 public void actionPerformed(ActionEvent e)
922 normaliseSequenceLogo_actionPerformed(e);
926 applyAutoAnnotationSettings
927 .setText(MessageManager.getString("label.apply_all_groups"));
928 applyAutoAnnotationSettings.setState(false);
929 applyAutoAnnotationSettings.setVisible(true);
930 applyAutoAnnotationSettings.addActionListener(new ActionListener()
933 public void actionPerformed(ActionEvent e)
935 applyAutoAnnotationSettings_actionPerformed(e);
939 ButtonGroup buttonGroup = new ButtonGroup();
940 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
941 MessageManager.getString("label.show_first"));
942 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
943 MessageManager.getString("label.show_last"));
944 buttonGroup.add(showAutoFirst);
945 buttonGroup.add(showAutoLast);
946 final boolean autoFirst = Cache
947 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
948 showAutoFirst.setSelected(autoFirst);
949 setShowAutoCalculatedAbove(autoFirst);
950 showAutoFirst.addActionListener(new ActionListener()
953 public void actionPerformed(ActionEvent e)
955 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
956 sortAnnotations_actionPerformed();
959 showAutoLast.setSelected(!showAutoFirst.isSelected());
960 showAutoLast.addActionListener(new ActionListener()
963 public void actionPerformed(ActionEvent e)
965 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
966 sortAnnotations_actionPerformed();
970 JMenuItem deleteGroups = new JMenuItem(
971 MessageManager.getString("action.undefine_groups"));
972 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
973 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
974 al = new ActionListener()
977 public void actionPerformed(ActionEvent e)
979 deleteGroups_actionPerformed(e);
982 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
984 JMenuItem annotationColumn = new JMenuItem(
985 MessageManager.getString("action.select_by_annotation"));
986 annotationColumn.addActionListener(new ActionListener()
989 public void actionPerformed(ActionEvent e)
991 annotationColumn_actionPerformed(e);
995 JMenuItem createGroup = new JMenuItem(
996 MessageManager.getString("action.create_group"));
997 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
998 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
999 al = new ActionListener()
1002 public void actionPerformed(ActionEvent e)
1004 createGroup_actionPerformed(e);
1007 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1009 JMenuItem unGroup = new JMenuItem(
1010 MessageManager.getString("action.remove_group"));
1011 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
1012 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1013 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1015 al = new ActionListener()
1018 public void actionPerformed(ActionEvent e)
1020 unGroup_actionPerformed(e);
1023 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1025 copy.setText(MessageManager.getString("action.copy"));
1026 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1027 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1029 al = new ActionListener()
1032 public void actionPerformed(ActionEvent e)
1034 copy_actionPerformed(e);
1037 addMenuActionAndAccelerator(keyStroke, copy, al);
1039 cut.setText(MessageManager.getString("action.cut"));
1040 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1041 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1042 al = new ActionListener()
1045 public void actionPerformed(ActionEvent e)
1047 cut_actionPerformed(e);
1050 addMenuActionAndAccelerator(keyStroke, cut, al);
1052 JMenuItem delete = new JMenuItem(
1053 MessageManager.getString("action.delete"));
1054 delete.addActionListener(new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 delete_actionPerformed(e);
1063 pasteMenu.setText(MessageManager.getString("action.paste"));
1064 JMenuItem pasteNew = new JMenuItem(
1065 MessageManager.getString("label.to_new_alignment"));
1066 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1067 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1068 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1070 al = new ActionListener()
1073 public void actionPerformed(ActionEvent e)
1077 pasteNew_actionPerformed(e);
1078 } catch (IOException | InterruptedException e1)
1080 // TODO Auto-generated catch block
1081 e1.printStackTrace();
1085 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1087 JMenuItem pasteThis = new JMenuItem(
1088 MessageManager.getString("label.to_this_alignment"));
1089 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1090 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1091 al = new ActionListener()
1094 public void actionPerformed(ActionEvent e)
1098 pasteThis_actionPerformed(e);
1099 } catch (IOException | InterruptedException e1)
1101 // TODO Auto-generated catch block
1102 e1.printStackTrace();
1106 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1108 JMenuItem createPNG = new JMenuItem("PNG");
1109 createPNG.addActionListener(new ActionListener()
1112 public void actionPerformed(ActionEvent e)
1117 createPNG.setActionCommand(
1118 MessageManager.getString("label.save_png_image"));
1119 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1120 font.addActionListener(new ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 font_actionPerformed(e);
1129 MessageManager.getString("label.show_sequence_limits"));
1130 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1131 seqLimits.addActionListener(new ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 seqLimit_actionPerformed(e);
1139 JMenuItem epsFile = new JMenuItem("EPS");
1140 epsFile.addActionListener(new ActionListener()
1143 public void actionPerformed(ActionEvent e)
1149 JMenuItem createSVG = new JMenuItem("SVG");
1150 createSVG.addActionListener(new ActionListener()
1153 public void actionPerformed(ActionEvent e)
1159 JMenuItem loadTreeMenuItem = new JMenuItem(
1160 MessageManager.getString("label.load_associated_tree"));
1161 loadTreeMenuItem.setActionCommand(
1162 MessageManager.getString("label.load_tree_for_sequence_set"));
1163 loadTreeMenuItem.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 loadTreeMenuItem_actionPerformed(e);
1172 scaleAbove.setVisible(false);
1173 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1174 scaleAbove.addActionListener(new ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 scaleAbove_actionPerformed(e);
1182 scaleLeft.setVisible(false);
1183 scaleLeft.setSelected(true);
1184 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1185 scaleLeft.addActionListener(new ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 scaleLeft_actionPerformed(e);
1193 scaleRight.setVisible(false);
1194 scaleRight.setSelected(true);
1195 scaleRight.setText(MessageManager.getString("action.scale_right"));
1196 scaleRight.addActionListener(new ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 scaleRight_actionPerformed(e);
1204 centreColumnLabelsMenuItem.setVisible(true);
1205 centreColumnLabelsMenuItem.setState(false);
1206 centreColumnLabelsMenuItem.setText(
1207 MessageManager.getString("label.centre_column_labels"));
1208 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 centreColumnLabels_actionPerformed(e);
1216 followHighlightMenuItem.setVisible(true);
1217 followHighlightMenuItem.setState(true);
1218 followHighlightMenuItem
1219 .setText(MessageManager.getString("label.automatic_scrolling"));
1220 followHighlightMenuItem.addActionListener(new ActionListener()
1224 public void actionPerformed(ActionEvent e)
1226 followHighlight_actionPerformed();
1232 .setText(MessageManager.getString("action.by_tree_order"));
1233 sort.setText(MessageManager.getString("action.sort"));
1234 sort.addMenuListener(new MenuListener()
1237 public void menuSelected(MenuEvent e)
1239 buildTreeSortMenu();
1243 public void menuDeselected(MenuEvent e)
1248 public void menuCanceled(MenuEvent e)
1253 .setText(MessageManager.getString("label.sort_by_score"));
1254 sort.add(sortByAnnotScore);
1255 sort.addMenuListener(new javax.swing.event.MenuListener()
1259 public void menuCanceled(MenuEvent e)
1264 public void menuDeselected(MenuEvent e)
1269 public void menuSelected(MenuEvent e)
1271 buildSortByAnnotationScoresMenu();
1274 sortByAnnotScore.setVisible(false);
1277 .setText(MessageManager.getString("action.calculate_tree_pca"));
1279 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1281 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1282 padGapsMenuitem.addActionListener(new ActionListener()
1285 public void actionPerformed(ActionEvent e)
1287 padGapsMenuitem_actionPerformed(e);
1290 JMenuItem vamsasStore = new JMenuItem(
1291 MessageManager.getString("label.vamsas_store"));
1292 vamsasStore.setVisible(false);
1293 vamsasStore.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 vamsasStore_actionPerformed(e);
1303 * Translate as cDNA with sub-menu of translation tables
1305 showTranslation.setText(MessageManager
1306 .getString("label.translate_cDNA"));
1307 boolean first = true;
1308 for (final GeneticCodeI table : GeneticCodes.getInstance()
1311 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1312 showTranslation.add(item);
1313 item.addActionListener(new ActionListener()
1316 public void actionPerformed(ActionEvent e)
1318 showTranslation_actionPerformed(table);
1323 showTranslation.addSeparator();
1328 showReverse.setText(MessageManager.getString("label.reverse"));
1329 showReverse.addActionListener(new ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 showReverse_actionPerformed(false);
1337 showReverseComplement
1338 .setText(MessageManager.getString("label.reverse_complement"));
1339 showReverseComplement.addActionListener(new ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 showReverse_actionPerformed(true);
1348 JMenuItem extractScores = new JMenuItem(
1349 MessageManager.getString("label.extract_scores"));
1350 extractScores.addActionListener(new ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 extractScores_actionPerformed(e);
1358 extractScores.setVisible(true);
1359 // JBPNote: TODO: make gui for regex based score extraction
1361 // for show products actions see AlignFrame.canShowProducts
1362 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1364 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1365 runGroovy.setToolTipText(
1366 MessageManager.getString("label.run_groovy_tip"));
1367 runGroovy.addActionListener(new ActionListener()
1370 public void actionPerformed(ActionEvent e)
1372 runGroovy_actionPerformed();
1376 JMenuItem openFeatureSettings = new JMenuItem(
1377 MessageManager.getString("action.feature_settings"));
1378 openFeatureSettings.addActionListener(new ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 featureSettings_actionPerformed(e);
1386 JMenuItem fetchSequence = new JMenuItem(
1387 MessageManager.getString("label.fetch_sequences"));
1388 fetchSequence.addActionListener(new ActionListener()
1391 public void actionPerformed(ActionEvent e)
1393 fetchSequence_actionPerformed(e);
1397 JMenuItem associatedData = new JMenuItem(
1398 MessageManager.getString("label.load_features_annotations"));
1399 associatedData.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1406 associatedData_actionPerformed(e);
1407 } catch (IOException | InterruptedException e1)
1409 // TODO Auto-generated catch block
1410 e1.printStackTrace();
1414 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1415 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1416 loadVcf.addActionListener(new ActionListener()
1419 public void actionPerformed(ActionEvent e)
1421 loadVcf_actionPerformed();
1424 autoCalculate.setText(
1425 MessageManager.getString("label.autocalculate_consensus"));
1426 autoCalculate.setState(
1427 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1428 autoCalculate.addActionListener(new ActionListener()
1431 public void actionPerformed(ActionEvent e)
1433 autoCalculate_actionPerformed(e);
1437 MessageManager.getString("label.sort_alignment_new_tree"));
1438 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1439 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1441 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1442 sortByTree.addActionListener(new ActionListener()
1445 public void actionPerformed(ActionEvent e)
1447 sortByTreeOption_actionPerformed(e);
1451 listenToViewSelections.setText(
1452 MessageManager.getString("label.listen_for_selections"));
1453 listenToViewSelections
1454 .setToolTipText("<html>" + MessageManager.getString(
1455 "label.selections_mirror_selections_made_same_sequences_other_views"));
1456 listenToViewSelections.setState(false);
1457 listenToViewSelections.addActionListener(new ActionListener()
1460 public void actionPerformed(ActionEvent e)
1462 listenToViewSelections_actionPerformed(e);
1466 JMenu addSequenceMenu = new JMenu(
1467 MessageManager.getString("label.add_sequences"));
1468 JMenuItem addFromFile = new JMenuItem(
1469 MessageManager.getString("label.from_file"));
1470 addFromFile.addActionListener(new ActionListener()
1473 public void actionPerformed(ActionEvent e)
1475 addFromFile_actionPerformed(e);
1478 JMenuItem addFromText = new JMenuItem(
1479 MessageManager.getString("label.from_textbox"));
1480 addFromText.addActionListener(new ActionListener()
1483 public void actionPerformed(ActionEvent e)
1485 addFromText_actionPerformed(e);
1488 JMenuItem addFromURL = new JMenuItem(
1489 MessageManager.getString("label.from_url"));
1490 addFromURL.addActionListener(new ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 addFromURL_actionPerformed(e);
1498 JMenuItem exportFeatures = new JMenuItem(
1499 MessageManager.getString("label.export_features"));
1500 exportFeatures.addActionListener(new ActionListener()
1503 public void actionPerformed(ActionEvent e)
1505 exportFeatures_actionPerformed(e);
1508 JMenuItem exportAnnotations = new JMenuItem(
1509 MessageManager.getString("label.export_annotations"));
1510 exportAnnotations.addActionListener(new ActionListener()
1513 public void actionPerformed(ActionEvent e)
1515 exportAnnotations_actionPerformed(e);
1518 statusPanel.setLayout(new GridLayout());
1519 JMenuItem showAllSeqs = new JMenuItem(
1520 MessageManager.getString("label.all_sequences"));
1521 showAllSeqs.setToolTipText(
1522 MessageManager.getString("label.toggle_sequence_visibility"));
1523 showAllSeqs.addActionListener(new ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 showAllSeqs_actionPerformed(e);
1531 JMenuItem showAllColumns = new JMenuItem(
1532 MessageManager.getString("label.all_columns"));
1533 showAllColumns.setToolTipText(
1534 MessageManager.getString("label.toggle_columns_visibility"));
1535 showAllColumns.addActionListener(new ActionListener()
1538 public void actionPerformed(ActionEvent e)
1540 showAllColumns_actionPerformed(e);
1543 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1544 JMenuItem hideSelSequences = new JMenuItem(
1545 MessageManager.getString("label.selected_sequences"));
1546 hideSelSequences.setToolTipText(
1547 MessageManager.getString("label.toggle_sequence_visibility"));
1548 hideSelSequences.addActionListener(new ActionListener()
1551 public void actionPerformed(ActionEvent e)
1553 hideSelSequences_actionPerformed(e);
1556 JMenuItem hideSelColumns = new JMenuItem(
1557 MessageManager.getString("label.selected_columns"));
1558 hideSelColumns.setToolTipText(
1559 MessageManager.getString("label.toggle_columns_visibility"));
1560 hideSelColumns.addActionListener(new ActionListener()
1563 public void actionPerformed(ActionEvent e)
1565 hideSelColumns_actionPerformed(e);
1568 JMenuItem hideAllSelection = new JMenuItem(
1569 MessageManager.getString("label.selected_region"));
1570 hideAllSelection.addActionListener(new ActionListener()
1573 public void actionPerformed(ActionEvent e)
1575 hideAllSelection_actionPerformed(e);
1578 // TODO: should be hidden if no selection exists.
1579 JMenuItem hideAllButSelection = new JMenuItem(
1580 MessageManager.getString("label.all_but_selected_region"));
1581 hideAllButSelection.addActionListener(new ActionListener()
1584 public void actionPerformed(ActionEvent e)
1586 hideAllButSelection_actionPerformed(e);
1589 JMenuItem showAllhidden = new JMenuItem(
1590 MessageManager.getString("label.all_sequences_columns"));
1591 showAllhidden.setToolTipText(MessageManager
1592 .getString("label.toggles_visibility_hidden_selected_regions"));
1593 showAllhidden.addActionListener(new ActionListener()
1596 public void actionPerformed(ActionEvent e)
1598 showAllhidden_actionPerformed(e);
1601 hiddenMarkers.setText(
1602 MessageManager.getString("action.show_hidden_markers"));
1603 hiddenMarkers.addActionListener(new ActionListener()
1606 public void actionPerformed(ActionEvent e)
1608 hiddenMarkers_actionPerformed(e);
1612 JMenuItem invertColSel = new JMenuItem(
1613 MessageManager.getString("action.invert_column_selection"));
1614 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1615 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1616 | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1618 al = new ActionListener()
1621 public void actionPerformed(ActionEvent e)
1623 invertColSel_actionPerformed(e);
1626 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1628 showComplementMenuItem.setVisible(false);
1629 showComplementMenuItem.addActionListener(new ActionListener()
1632 public void actionPerformed(ActionEvent e)
1634 showComplement_actionPerformed(showComplementMenuItem.getState());
1638 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1641 public void stateChanged(ChangeEvent evt)
1643 JTabbedPane pane = (JTabbedPane) evt.getSource();
1644 int sel = pane.getSelectedIndex();
1645 tabSelectionChanged(sel);
1648 tabbedPane.addMouseListener(new MouseAdapter()
1651 public void mousePressed(MouseEvent e)
1653 if (e.isPopupTrigger()) // Mac
1655 tabbedPane_mousePressed(e);
1660 public void mouseReleased(MouseEvent e)
1662 if (e.isPopupTrigger()) // Windows
1664 tabbedPane_mousePressed(e);
1668 tabbedPane.addFocusListener(new FocusAdapter()
1671 public void focusGained(FocusEvent e)
1673 tabbedPane_focusGained(e);
1677 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1678 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1679 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1680 al = new ActionListener()
1683 public void actionPerformed(ActionEvent e)
1685 save_actionPerformed(e);
1688 addMenuActionAndAccelerator(keyStroke, save, al);
1690 reload.setEnabled(false);
1691 reload.setText(MessageManager.getString("action.reload"));
1692 reload.addActionListener(new ActionListener()
1695 public void actionPerformed(ActionEvent e)
1697 reload_actionPerformed(e);
1701 JMenuItem newView = new JMenuItem(
1702 MessageManager.getString("action.new_view"));
1703 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1704 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1705 al = new ActionListener()
1708 public void actionPerformed(ActionEvent e)
1710 newView_actionPerformed(e);
1713 addMenuActionAndAccelerator(keyStroke, newView, al);
1715 tabbedPane.setToolTipText("<html><i>"
1716 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1719 formatMenu.setText(MessageManager.getString("action.format"));
1720 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1722 idRightAlign.setText(
1723 MessageManager.getString("label.right_align_sequence_id"));
1724 idRightAlign.addActionListener(new ActionListener()
1727 public void actionPerformed(ActionEvent e)
1729 idRightAlign_actionPerformed(e);
1733 gatherViews.setEnabled(false);
1734 gatherViews.setText(MessageManager.getString("action.gather_views"));
1735 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1736 al = new ActionListener()
1739 public void actionPerformed(ActionEvent e)
1741 gatherViews_actionPerformed(e);
1744 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1746 expandViews.setEnabled(false);
1747 expandViews.setText(MessageManager.getString("action.expand_views"));
1748 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1749 al = new ActionListener()
1752 public void actionPerformed(ActionEvent e)
1754 expandViews_actionPerformed(e);
1757 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1759 JMenuItem pageSetup = new JMenuItem(
1760 MessageManager.getString("action.page_setup"));
1761 pageSetup.addActionListener(new ActionListener()
1764 public void actionPerformed(ActionEvent e)
1766 pageSetup_actionPerformed(e);
1769 JMenuItem alignmentProperties = new JMenuItem(
1770 MessageManager.getString("label.alignment_props"));
1771 alignmentProperties.addActionListener(new ActionListener()
1774 public void actionPerformed(ActionEvent actionEvent)
1776 alignmentProperties();
1779 JMenuItem selectHighlighted = new JMenuItem(
1780 MessageManager.getString("action.select_highlighted_columns"));
1781 selectHighlighted.setToolTipText(
1782 MessageManager.getString("tooltip.select_highlighted_columns"));
1783 al = new ActionListener()
1786 public void actionPerformed(ActionEvent actionEvent)
1788 selectHighlightedColumns_actionPerformed(actionEvent);
1791 JMenuItem Filter = new JMenuItem(
1792 MessageManager.getString("action.select_highlighted_columns"));
1793 selectHighlighted.setToolTipText(
1794 MessageManager.getString("tooltip.select_highlighted_columns"));
1795 al = new ActionListener()
1798 public void actionPerformed(ActionEvent actionEvent)
1800 selectHighlightedColumns_actionPerformed(actionEvent);
1803 selectHighlighted.addActionListener(al);
1804 JMenu tooltipSettingsMenu = new JMenu(
1805 MessageManager.getString("label.sequence_id_tooltip"));
1806 JMenu autoAnnMenu = new JMenu(
1807 MessageManager.getString("label.autocalculated_annotation"));
1809 JMenu exportImageMenu = new JMenu(
1810 MessageManager.getString("label.export_image"));
1811 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1812 alignFrameMenuBar.add(fileMenu);
1813 alignFrameMenuBar.add(editMenu);
1814 alignFrameMenuBar.add(selectMenu);
1815 alignFrameMenuBar.add(viewMenu);
1816 alignFrameMenuBar.add(annotationsMenu);
1817 alignFrameMenuBar.add(formatMenu);
1818 alignFrameMenuBar.add(colourMenu);
1819 alignFrameMenuBar.add(calculateMenu);
1820 alignFrameMenuBar.add(webService);
1821 alignFrameMenuBar.add(hmmerMenu);
1823 fileMenu.add(fetchSequence);
1824 fileMenu.add(addSequenceMenu);
1825 fileMenu.add(reload);
1826 fileMenu.addSeparator();
1827 fileMenu.add(vamsasStore);
1829 fileMenu.add(saveAs);
1830 fileMenu.add(outputTextboxMenu);
1831 fileMenu.add(pageSetup);
1832 fileMenu.add(printMenuItem);
1833 fileMenu.addSeparator();
1834 fileMenu.add(exportImageMenu);
1835 fileMenu.add(exportFeatures);
1836 fileMenu.add(exportAnnotations);
1837 fileMenu.add(loadTreeMenuItem);
1838 fileMenu.add(associatedData);
1839 fileMenu.add(loadVcf);
1840 fileMenu.addSeparator();
1841 fileMenu.add(closeMenuItem);
1843 pasteMenu.add(pasteNew);
1844 pasteMenu.add(pasteThis);
1845 editMenu.add(undoMenuItem);
1846 editMenu.add(redoMenuItem);
1849 editMenu.add(pasteMenu);
1850 editMenu.add(delete);
1851 editMenu.addSeparator();
1852 editMenu.add(remove2LeftMenuItem);
1853 editMenu.add(remove2RightMenuItem);
1854 editMenu.add(removeGappedColumnMenuItem);
1855 editMenu.add(removeAllGapsMenuItem);
1856 editMenu.add(removeRedundancyMenuItem);
1857 editMenu.addSeparator();
1858 // dont add these yet in the CVS build - they cannot be undone!
1859 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1860 // editMenu.add(justifyLeftMenuItem);
1861 // editMenu.add(justifyRightMenuItem);
1862 // editMenu.addSeparator();
1863 editMenu.add(padGapsMenuitem);
1864 editMenu.addSeparator();
1865 editMenu.add(filterByEValue);
1866 editMenu.add(filterByScore);
1868 showMenu.add(showAllColumns);
1869 showMenu.add(showAllSeqs);
1870 showMenu.add(showAllhidden);
1871 hideMenu.add(hideSelColumns);
1872 hideMenu.add(hideSelSequences);
1873 hideMenu.add(hideAllSelection);
1874 hideMenu.add(hideAllButSelection);
1875 viewMenu.add(newView);
1876 viewMenu.add(expandViews);
1877 viewMenu.add(gatherViews);
1878 viewMenu.addSeparator();
1879 viewMenu.add(showMenu);
1880 viewMenu.add(hideMenu);
1881 viewMenu.add(showComplementMenuItem);
1882 viewMenu.addSeparator();
1883 viewMenu.add(followHighlightMenuItem);
1884 viewMenu.addSeparator();
1885 viewMenu.add(showSeqFeatures);
1886 // viewMenu.add(showSeqFeaturesHeight);
1887 viewMenu.add(openFeatureSettings);
1888 tooltipSettingsMenu.add(showDbRefsMenuitem);
1889 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1890 viewMenu.add(tooltipSettingsMenu);
1891 viewMenu.addSeparator();
1892 viewMenu.add(alignmentProperties);
1893 viewMenu.addSeparator();
1894 viewMenu.add(overviewMenuItem);
1896 annotationsMenu.add(annotationPanelMenuItem);
1897 annotationsMenu.addSeparator();
1898 annotationsMenu.add(showAllAlAnnotations);
1899 annotationsMenu.add(hideAllAlAnnotations);
1900 annotationsMenu.addSeparator();
1901 annotationsMenu.add(showAllSeqAnnotations);
1902 annotationsMenu.add(hideAllSeqAnnotations);
1903 annotationsMenu.add(sortAnnBySequence);
1904 annotationsMenu.add(sortAnnByLabel);
1905 annotationsMenu.addSeparator();
1906 autoAnnMenu.add(showAutoFirst);
1907 autoAnnMenu.add(showAutoLast);
1908 autoAnnMenu.addSeparator();
1909 autoAnnMenu.add(applyAutoAnnotationSettings);
1910 autoAnnMenu.add(showConsensusHistogram);
1911 autoAnnMenu.add(showSequenceLogo);
1912 autoAnnMenu.add(normaliseSequenceLogo);
1913 autoAnnMenu.addSeparator();
1914 autoAnnMenu.add(showGroupConservation);
1915 autoAnnMenu.add(showGroupConsensus);
1916 annotationsMenu.add(autoAnnMenu);
1918 sort.add(sortIDMenuItem);
1919 sort.add(sortLengthMenuItem);
1920 sort.add(sortGroupMenuItem);
1921 sort.add(sortPairwiseMenuItem);
1922 sort.add(sortEValueMenuItem);
1923 sort.add(sortBitScoreMenuItem);
1924 sort.add(sortByTreeMenu);
1925 calculateMenu.add(sort);
1926 calculateMenu.add(calculateTree);
1927 calculateMenu.addSeparator();
1928 calculateMenu.add(pairwiseAlignmentMenuItem);
1929 calculateMenu.addSeparator();
1930 calculateMenu.add(showTranslation);
1931 calculateMenu.add(showReverse);
1932 calculateMenu.add(showReverseComplement);
1933 calculateMenu.add(showProducts);
1934 calculateMenu.add(autoCalculate);
1935 calculateMenu.add(sortByTree);
1936 calculateMenu.addSeparator();
1937 calculateMenu.add(expandAlignment);
1938 calculateMenu.add(extractScores);
1939 calculateMenu.addSeparator();
1940 calculateMenu.add(runGroovy);
1942 webServiceNoServices = new JMenuItem(
1943 MessageManager.getString("label.no_services"));
1944 webService.add(webServiceNoServices);
1945 exportImageMenu.add(htmlMenuItem);
1946 exportImageMenu.add(epsFile);
1947 exportImageMenu.add(createPNG);
1948 exportImageMenu.add(createBioJS);
1949 exportImageMenu.add(createSVG);
1950 addSequenceMenu.add(addFromFile);
1951 addSequenceMenu.add(addFromText);
1952 addSequenceMenu.add(addFromURL);
1953 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1954 statusPanel.add(statusBar, null);
1955 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1957 formatMenu.add(font);
1958 formatMenu.addSeparator();
1959 formatMenu.add(wrapMenuItem);
1960 formatMenu.add(scaleAbove);
1961 formatMenu.add(scaleLeft);
1962 formatMenu.add(scaleRight);
1963 formatMenu.add(seqLimits);
1964 formatMenu.add(idRightAlign);
1965 formatMenu.add(hiddenMarkers);
1966 formatMenu.add(viewBoxesMenuItem);
1967 formatMenu.add(viewTextMenuItem);
1968 formatMenu.add(colourTextMenuItem);
1969 formatMenu.add(renderGapsMenuItem);
1970 formatMenu.add(centreColumnLabelsMenuItem);
1971 formatMenu.add(showNonconservedMenuItem);
1972 selectMenu.add(findMenuItem);
1973 selectMenu.addSeparator();
1974 selectMenu.add(selectAllSequenceMenuItem);
1975 selectMenu.add(deselectAllSequenceMenuItem);
1976 selectMenu.add(invertSequenceMenuItem);
1977 selectMenu.add(invertColSel);
1978 selectMenu.add(createGroup);
1979 selectMenu.add(unGroup);
1980 selectMenu.add(grpsFromSelection);
1981 selectMenu.add(deleteGroups);
1982 selectMenu.add(annotationColumn);
1983 selectMenu.add(selectHighlighted);
1984 // TODO - determine if the listenToViewSelections button is needed : see bug
1986 // selectMenu.addSeparator();
1987 // selectMenu.add(listenToViewSelections);
1991 * Constructs the entries on the HMMER menu
1993 protected void initHMMERMenu()
1998 JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
1999 JMenuItem hmmBuildSettings = new JMenuItem(
2000 MessageManager.getString("label.edit_settings_and_run"));
2001 hmmBuildSettings.addActionListener(new ActionListener()
2004 public void actionPerformed(ActionEvent e)
2006 hmmBuild_actionPerformed(false);
2009 JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
2010 "label.action_with_default_settings", "hmmbuild"));
2011 hmmBuildRun.addActionListener(new ActionListener()
2014 public void actionPerformed(ActionEvent e)
2016 hmmBuild_actionPerformed(true);
2019 hmmBuild.add(hmmBuildRun);
2020 hmmBuild.add(hmmBuildSettings);
2025 JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
2026 JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
2027 "label.action_with_default_settings", "hmmalign"));
2028 hmmAlignRun.addActionListener(new ActionListener()
2031 public void actionPerformed(ActionEvent e)
2033 hmmAlign_actionPerformed(true);
2036 JMenuItem hmmAlignSettings = new JMenuItem(
2037 MessageManager.getString("label.edit_settings_and_run"));
2038 hmmAlignSettings.addActionListener(new ActionListener()
2041 public void actionPerformed(ActionEvent e)
2043 hmmAlign_actionPerformed(false);
2046 hmmAlign.add(hmmAlignRun);
2047 hmmAlign.add(hmmAlignSettings);
2052 JMenu hmmSearch = new JMenu(
2053 MessageManager.getString("label.hmmsearch"));
2054 JMenuItem hmmSearchSettings = new JMenuItem(
2055 MessageManager.getString("label.edit_settings_and_run"));
2056 hmmSearchSettings.addActionListener(new ActionListener()
2059 public void actionPerformed(ActionEvent e)
2061 hmmSearch_actionPerformed(false);
2064 JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
2065 "label.action_with_default_settings", "hmmsearch"));
2066 hmmSearchRun.addActionListener(new ActionListener()
2069 public void actionPerformed(ActionEvent e)
2071 hmmSearch_actionPerformed(true);
2074 JMenuItem addDatabase = new JMenuItem(
2075 MessageManager.getString("label.add_database"));
2076 addDatabase.addActionListener(new ActionListener()
2079 public void actionPerformed(ActionEvent e)
2083 addDatabase_actionPerformed();
2084 } catch (IOException e1)
2086 e1.printStackTrace();
2090 hmmSearch.add(hmmSearchRun);
2091 hmmSearch.add(hmmSearchSettings);
2092 // hmmSearch.add(addDatabase);
2097 JMenu jackhmmer = new JMenu(
2098 MessageManager.getString("label.jackhmmer"));
2099 JMenuItem jackhmmerSettings = new JMenuItem(
2100 MessageManager.getString("label.edit_settings_and_run"));
2101 jackhmmerSettings.addActionListener(new ActionListener()
2104 public void actionPerformed(ActionEvent e)
2106 jackhmmer_actionPerformed(false);
2109 JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage(
2110 "label.action_with_default_settings", "jackhmmer"));
2111 jackhmmerRun.addActionListener(new ActionListener()
2114 public void actionPerformed(ActionEvent e)
2116 jackhmmer_actionPerformed(true);
2121 JMenuItem addDatabase = new JMenuItem(
2122 MessageManager.getString("label.add_database"));
2123 addDatabase.addActionListener(new ActionListener()
2126 public void actionPerformed(ActionEvent e)
2130 addDatabase_actionPerformed();
2131 } catch (IOException e1)
2133 e1.printStackTrace();
2138 jackhmmer.add(jackhmmerRun);
2139 jackhmmer.add(jackhmmerSettings);
2140 // hmmSearch.add(addDatabase);
2145 hmmerMenu.setText(MessageManager.getString("action.hmmer"));
2146 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
2147 hmmerMenu.add(hmmBuild);
2148 hmmerMenu.add(hmmAlign);
2149 hmmerMenu.add(hmmSearch);
2150 hmmerMenu.add(jackhmmer);
2154 protected void loadVcf_actionPerformed()
2159 * Constructs the entries on the Colour menu (but does not add them to the
2162 protected void initColourMenu()
2164 applyToAllGroups = new JCheckBoxMenuItem(
2165 MessageManager.getString("label.apply_colour_to_all_groups"));
2166 applyToAllGroups.addActionListener(new ActionListener()
2169 public void actionPerformed(ActionEvent e)
2171 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2175 textColour = new JMenuItem(
2176 MessageManager.getString("label.text_colour"));
2177 textColour.addActionListener(new ActionListener()
2180 public void actionPerformed(ActionEvent e)
2182 textColour_actionPerformed();
2186 conservationMenuItem = new JCheckBoxMenuItem(
2187 MessageManager.getString("action.by_conservation"));
2188 conservationMenuItem.addActionListener(new ActionListener()
2191 public void actionPerformed(ActionEvent e)
2193 conservationMenuItem_actionPerformed(
2194 conservationMenuItem.isSelected());
2198 abovePIDThreshold = new JCheckBoxMenuItem(
2199 MessageManager.getString("label.above_identity_threshold"));
2200 abovePIDThreshold.addActionListener(new ActionListener()
2203 public void actionPerformed(ActionEvent e)
2205 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2208 modifyPID = new JMenuItem(
2209 MessageManager.getString("label.modify_identity_threshold"));
2210 modifyPID.addActionListener(new ActionListener()
2213 public void actionPerformed(ActionEvent e)
2215 modifyPID_actionPerformed();
2218 modifyConservation = new JMenuItem(MessageManager
2219 .getString("label.modify_conservation_threshold"));
2220 modifyConservation.addActionListener(new ActionListener()
2223 public void actionPerformed(ActionEvent e)
2225 modifyConservation_actionPerformed();
2229 annotationColour = new JRadioButtonMenuItem(
2230 MessageManager.getString("action.by_annotation"));
2231 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2232 annotationColour.addActionListener(new ActionListener()
2235 public void actionPerformed(ActionEvent e)
2237 annotationColour_actionPerformed();
2242 protected void selectHighlightedColumns_actionPerformed(
2243 ActionEvent actionEvent)
2245 // TODO Auto-generated method stub
2250 * Generate the reverse sequence (or reverse complement if the flag is true)
2251 * and add it to the alignment
2255 protected void showReverse_actionPerformed(boolean complement)
2260 * Try to run script in a Groovy console, having first ensured that this
2261 * alignframe is set as currentAlignFrame in Desktop
2263 protected void runGroovy_actionPerformed()
2269 * Adds the given action listener and key accelerator to the given menu item.
2270 * Also saves in a lookup table to support lookup of action by key stroke.
2274 * @param actionListener
2276 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2277 JMenuItem menuItem, ActionListener actionListener)
2279 menuItem.setAccelerator(keyStroke);
2280 accelerators.put(keyStroke, menuItem);
2281 menuItem.addActionListener(actionListener);
2285 * Action on clicking sort annotations by type.
2289 protected void sortAnnotations_actionPerformed()
2294 * Action on clicking Show all annotations.
2296 * @param forSequences
2297 * update sequence-related annotations
2298 * @param forAlignment
2299 * update non-sequence-related annotations
2301 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2302 boolean forAlignment)
2304 setAnnotationsVisibility(true, forSequences, forAlignment);
2308 * Action on clicking Hide all annotations.
2310 * @param forSequences
2311 * update sequence-related annotations
2312 * @param forAlignment
2313 * update non-sequence-related annotations
2315 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2316 boolean forAlignment)
2318 setAnnotationsVisibility(false, forSequences, forAlignment);
2322 * Set the visibility of annotations to true or false. Can act on
2323 * sequence-related annotations, or alignment-related, or both.
2326 * @param forSequences
2327 * update sequence-related annotations
2328 * @param forAlignment
2329 * update non-sequence-related annotations
2331 protected void setAnnotationsVisibility(boolean visible,
2332 boolean forSequences, boolean forAlignment)
2337 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2339 // TODO Auto-generated method stub
2343 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2345 // TODO Auto-generated method stub
2349 protected void showAllhidden_actionPerformed(ActionEvent e)
2351 // TODO Auto-generated method stub
2355 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2357 // TODO Auto-generated method stub
2361 protected void hideAllSelection_actionPerformed(ActionEvent e)
2363 // TODO Auto-generated method stub
2367 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2369 // TODO Auto-generated method stub
2373 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2375 // TODO Auto-generated method stub
2379 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2381 // TODO Auto-generated method stub
2385 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2387 // TODO Auto-generated method stub
2391 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2393 // TODO Auto-generated method stub
2397 protected void showGroupConservation_actionPerformed(ActionEvent e)
2399 // TODO Auto-generated method stub
2403 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2405 // TODO Auto-generated method stub
2409 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2411 // TODO Auto-generated method stub
2415 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2417 // TODO Auto-generated method stub
2421 protected void followHighlight_actionPerformed()
2423 // TODO Auto-generated method stub
2427 protected void showNpFeats_actionPerformed(ActionEvent e)
2429 // TODO Auto-generated method stub
2433 protected void showDbRefs_actionPerformed(ActionEvent e)
2435 // TODO Auto-generated method stub
2439 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2443 protected void buildSortByAnnotationScoresMenu()
2447 protected void extractScores_actionPerformed(ActionEvent e)
2451 protected void outputText_actionPerformed(ActionEvent e)
2455 public void addFromFile_actionPerformed(ActionEvent e)
2460 public void addFromText_actionPerformed(ActionEvent e)
2465 public void addFromURL_actionPerformed(ActionEvent e)
2470 public void exportFeatures_actionPerformed(ActionEvent e)
2475 public void exportAnnotations_actionPerformed(ActionEvent e)
2480 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2484 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2489 protected void closeMenuItem_actionPerformed(boolean b)
2493 protected void redoMenuItem_actionPerformed(ActionEvent e)
2497 protected void undoMenuItem_actionPerformed(ActionEvent e)
2501 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2505 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2509 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2513 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2517 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2521 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2525 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2529 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2533 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2537 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2541 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2545 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2549 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2553 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2557 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2561 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2565 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2569 protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
2573 protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
2577 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2581 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2585 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2589 protected void conservationMenuItem_actionPerformed(boolean selected)
2593 protected void printMenuItem_actionPerformed(ActionEvent e)
2597 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2601 protected void findMenuItem_actionPerformed(ActionEvent e)
2605 protected void abovePIDThreshold_actionPerformed(boolean selected)
2609 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2613 protected void deleteGroups_actionPerformed(ActionEvent e)
2617 protected void createGroup_actionPerformed(ActionEvent e)
2621 protected void unGroup_actionPerformed(ActionEvent e)
2625 protected void copy_actionPerformed(ActionEvent e)
2629 protected void cut_actionPerformed(ActionEvent e)
2633 protected void delete_actionPerformed(ActionEvent e)
2637 protected void pasteNew_actionPerformed(ActionEvent e)
2638 throws IOException, InterruptedException
2642 protected void pasteThis_actionPerformed(ActionEvent e)
2643 throws IOException, InterruptedException
2647 protected void applyToAllGroups_actionPerformed(boolean selected)
2651 protected void hmmBuild_actionPerformed(boolean withDefaults)
2655 protected void hmmSearch_actionPerformed(boolean withDefaults)
2659 protected void jackhmmer_actionPerformed(boolean b)
2663 protected void addDatabase_actionPerformed()
2664 throws FileFormatException, IOException
2668 protected void hmmAlign_actionPerformed(boolean withDefaults)
2672 public void createPNG(java.io.File f)
2676 protected void font_actionPerformed(ActionEvent e)
2680 protected void seqLimit_actionPerformed(ActionEvent e)
2684 public void seqDBRef_actionPerformed(ActionEvent e)
2689 public void createEPS(java.io.File f)
2693 public void createSVG(java.io.File f)
2698 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2704 * Template method to handle the 'load T-Coffee scores' menu event.
2706 * Subclasses override this method to provide a custom action.
2711 protected void loadScores_actionPerformed(ActionEvent event)
2716 protected void jpred_actionPerformed(ActionEvent e)
2720 protected void scaleAbove_actionPerformed(ActionEvent e)
2724 protected void scaleLeft_actionPerformed(ActionEvent e)
2728 protected void filterByEValue_actionPerformed()
2732 protected void filterByScore_actionPerformed()
2736 protected void scaleRight_actionPerformed(ActionEvent e)
2740 protected void modifyPID_actionPerformed()
2744 protected void modifyConservation_actionPerformed()
2748 protected void saveAs_actionPerformed(ActionEvent e)
2752 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2756 public void vamsasStore_actionPerformed(ActionEvent e)
2761 public void vamsasLoad_actionPerformed(ActionEvent e)
2766 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2771 public void featureSettings_actionPerformed(ActionEvent e)
2776 public void fetchSequence_actionPerformed(ActionEvent e)
2781 public void smoothFont_actionPerformed(ActionEvent e)
2786 public void annotationColour_actionPerformed()
2790 public void annotationColumn_actionPerformed(ActionEvent e)
2794 public void associatedData_actionPerformed(ActionEvent e)
2795 throws IOException, InterruptedException
2800 public void autoCalculate_actionPerformed(ActionEvent e)
2805 public void sortByTreeOption_actionPerformed(ActionEvent e)
2810 public void showAllSeqs_actionPerformed(ActionEvent e)
2815 public void showAllColumns_actionPerformed(ActionEvent e)
2820 public void hideSelSequences_actionPerformed(ActionEvent e)
2825 public void hideSelColumns_actionPerformed(ActionEvent e)
2830 public void hiddenMarkers_actionPerformed(ActionEvent e)
2835 public void findPdbId_actionPerformed(ActionEvent e)
2840 public void enterPdbId_actionPerformed(ActionEvent e)
2845 public void pdbFile_actionPerformed(ActionEvent e)
2850 public void invertColSel_actionPerformed(ActionEvent e)
2855 public void tabSelectionChanged(int sel)
2860 public void tabbedPane_mousePressed(MouseEvent e)
2865 public void tabbedPane_focusGained(FocusEvent e)
2870 public void save_actionPerformed(ActionEvent e)
2875 public void reload_actionPerformed(ActionEvent e)
2880 public void newView_actionPerformed(ActionEvent e)
2885 public void textColour_actionPerformed()
2890 public void idRightAlign_actionPerformed(ActionEvent e)
2895 public void expandViews_actionPerformed(ActionEvent e)
2900 public void gatherViews_actionPerformed(ActionEvent e)
2905 public void buildTreeSortMenu()
2910 public void pageSetup_actionPerformed(ActionEvent e)
2915 public void alignmentProperties()
2920 protected void expand_newalign(ActionEvent e)
2922 // TODO Auto-generated method stub
2926 protected boolean isShowAutoCalculatedAbove()
2928 return showAutoCalculatedAbove;
2931 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2933 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2936 protected SequenceAnnotationOrder getAnnotationSortOrder()
2938 return annotationSortOrder;
2941 protected void setAnnotationSortOrder(
2942 SequenceAnnotationOrder annotationSortOrder)
2944 this.annotationSortOrder = annotationSortOrder;
2947 public Map<KeyStroke, JMenuItem> getAccelerators()
2949 return this.accelerators;
2953 * Returns the selected index of the tabbed pane, or -1 if none selected
2954 * (including the case where the tabbed pane has not been made visible).
2958 public int getTabIndex()
2960 return tabbedPane.getSelectedIndex();
2963 public JPanel getStatusPanel()
2969 * Sets a reference to the containing split frame. Also makes the 'toggle
2970 * split view' menu item visible and checked.
2974 public void setSplitFrame(SplitContainerI sf)
2976 this.splitFrame = sf;
2979 this.showComplementMenuItem.setVisible(true);
2980 this.showComplementMenuItem.setState(true);
2984 public SplitContainerI getSplitViewContainer()
2986 return this.splitFrame;
2989 protected void showComplement_actionPerformed(boolean complement)