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);
522 JMenuItem removeRedundancyMenuItem = new JMenuItem(
523 MessageManager.getString("action.remove_redundancy"));
524 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
525 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
526 al = new ActionListener()
529 public void actionPerformed(ActionEvent e)
531 removeRedundancyMenuItem_actionPerformed(e);
534 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
536 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
537 MessageManager.getString("action.pairwise_alignment"));
538 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
541 public void actionPerformed(ActionEvent e)
543 pairwiseAlignmentMenuItem_actionPerformed(e);
547 this.getContentPane().setLayout(new BorderLayout());
548 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
549 statusBar.setBackground(Color.white);
550 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
551 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
552 statusBar.setText(MessageManager.getString("label.status_bar"));
555 .setText(MessageManager.getString("label.out_to_textbox"));
558 annotationPanelMenuItem.setActionCommand("");
559 annotationPanelMenuItem
560 .setText(MessageManager.getString("label.show_annotations"));
561 annotationPanelMenuItem
562 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
563 annotationPanelMenuItem.addActionListener(new ActionListener()
566 public void actionPerformed(ActionEvent e)
568 annotationPanelMenuItem_actionPerformed(e);
571 showAllAlAnnotations.setText(
572 MessageManager.getString("label.show_all_al_annotations"));
573 final boolean isAnnotationPanelShown = annotationPanelMenuItem
575 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
576 showAllAlAnnotations.addActionListener(new ActionListener()
579 public void actionPerformed(ActionEvent e)
581 showAllAnnotations_actionPerformed(false, true);
584 hideAllAlAnnotations.setText(
585 MessageManager.getString("label.hide_all_al_annotations"));
586 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
587 hideAllAlAnnotations.addActionListener(new ActionListener()
590 public void actionPerformed(ActionEvent e)
592 hideAllAnnotations_actionPerformed(false, true);
595 showAllSeqAnnotations.setText(
596 MessageManager.getString("label.show_all_seq_annotations"));
597 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
598 showAllSeqAnnotations.addActionListener(new ActionListener()
601 public void actionPerformed(ActionEvent e)
603 showAllAnnotations_actionPerformed(true, false);
606 hideAllSeqAnnotations.setText(
607 MessageManager.getString("label.hide_all_seq_annotations"));
608 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
609 hideAllSeqAnnotations.addActionListener(new ActionListener()
612 public void actionPerformed(ActionEvent e)
614 hideAllAnnotations_actionPerformed(true, false);
617 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
618 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
619 SequenceAnnotationOrder.NONE.name()));
620 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
621 MessageManager.getString("label.sort_annotations_by_sequence"));
622 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
623 MessageManager.getString("label.sort_annotations_by_label"));
626 sortAnnBySequence.setSelected(
627 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
628 sortAnnBySequence.addActionListener(new ActionListener()
631 public void actionPerformed(ActionEvent e)
633 boolean newState = sortAnnBySequence.getState();
634 sortAnnByLabel.setSelected(false);
635 setAnnotationSortOrder(
636 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
637 : SequenceAnnotationOrder.NONE);
638 sortAnnotations_actionPerformed();
641 sortAnnByLabel.setSelected(
642 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
643 sortAnnByLabel.addActionListener(new ActionListener()
646 public void actionPerformed(ActionEvent e)
648 boolean newState = sortAnnByLabel.getState();
649 sortAnnBySequence.setSelected(false);
650 setAnnotationSortOrder(
651 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
652 : SequenceAnnotationOrder.NONE);
653 sortAnnotations_actionPerformed();
656 colourTextMenuItem = new JCheckBoxMenuItem(
657 MessageManager.getString("label.colour_text"));
658 colourTextMenuItem.addActionListener(new ActionListener()
661 public void actionPerformed(ActionEvent e)
663 colourTextMenuItem_actionPerformed(e);
667 JMenuItem htmlMenuItem = new JMenuItem(
668 MessageManager.getString("label.html"));
669 htmlMenuItem.addActionListener(new ActionListener()
672 public void actionPerformed(ActionEvent e)
674 htmlMenuItem_actionPerformed(e);
678 JMenuItem createBioJS = new JMenuItem(
679 MessageManager.getString("label.biojs_html_export"));
680 createBioJS.addActionListener(new java.awt.event.ActionListener()
683 public void actionPerformed(ActionEvent e)
685 bioJSMenuItem_actionPerformed(e);
689 JMenuItem overviewMenuItem = new JMenuItem(
690 MessageManager.getString("label.overview_window"));
691 overviewMenuItem.addActionListener(new ActionListener()
694 public void actionPerformed(ActionEvent e)
696 overviewMenuItem_actionPerformed(e);
700 undoMenuItem.setEnabled(false);
701 undoMenuItem.setText(MessageManager.getString("action.undo"));
702 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
703 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
704 al = new ActionListener()
707 public void actionPerformed(ActionEvent e)
709 undoMenuItem_actionPerformed(e);
712 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
714 redoMenuItem.setEnabled(false);
715 redoMenuItem.setText(MessageManager.getString("action.redo"));
716 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
717 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
718 al = new ActionListener()
721 public void actionPerformed(ActionEvent e)
723 redoMenuItem_actionPerformed(e);
726 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
728 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
729 wrapMenuItem.addActionListener(new ActionListener()
732 public void actionPerformed(ActionEvent e)
734 wrapMenuItem_actionPerformed(e);
738 JMenuItem printMenuItem = new JMenuItem(
739 MessageManager.getString("action.print"));
740 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
741 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
742 al = new ActionListener()
745 public void actionPerformed(ActionEvent e)
747 printMenuItem_actionPerformed(e);
750 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
753 .setText(MessageManager.getString("action.show_gaps"));
754 renderGapsMenuItem.setState(true);
755 renderGapsMenuItem.addActionListener(new ActionListener()
758 public void actionPerformed(ActionEvent e)
760 renderGapsMenuItem_actionPerformed(e);
764 JMenuItem findMenuItem = new JMenuItem(
765 MessageManager.getString("action.find"));
766 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
767 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
768 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
769 MessageManager.getString("label.find_tip")));
770 al = new ActionListener()
773 public void actionPerformed(ActionEvent e)
775 findMenuItem_actionPerformed(e);
778 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
780 showSeqFeatures.setText(
781 MessageManager.getString("label.show_sequence_features"));
783 showSeqFeatures.addActionListener(new ActionListener()
786 public void actionPerformed(ActionEvent actionEvent)
788 showSeqFeatures_actionPerformed(actionEvent);
792 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
793 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
794 * void actionPerformed(ActionEvent actionEvent) {
795 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
798 .setText(MessageManager.getString("label.show_database_refs"));
799 showDbRefsMenuitem.addActionListener(new ActionListener()
803 public void actionPerformed(ActionEvent e)
805 showDbRefs_actionPerformed(e);
809 showNpFeatsMenuitem.setText(
810 MessageManager.getString("label.show_non_positional_features"));
811 showNpFeatsMenuitem.addActionListener(new ActionListener()
815 public void actionPerformed(ActionEvent e)
817 showNpFeats_actionPerformed(e);
821 showGroupConservation
822 .setText(MessageManager.getString("label.group_conservation"));
823 showGroupConservation.addActionListener(new ActionListener()
827 public void actionPerformed(ActionEvent e)
829 showGroupConservation_actionPerformed(e);
835 .setText(MessageManager.getString("label.group_consensus"));
836 showGroupConsensus.addActionListener(new ActionListener()
840 public void actionPerformed(ActionEvent e)
842 showGroupConsensus_actionPerformed(e);
846 showConsensusHistogram.setText(
847 MessageManager.getString("label.show_consensus_histogram"));
848 showConsensusHistogram.addActionListener(new ActionListener()
852 public void actionPerformed(ActionEvent e)
854 showConsensusHistogram_actionPerformed(e);
859 .setText(MessageManager.getString("label.show_consensus_logo"));
860 showSequenceLogo.addActionListener(new ActionListener()
864 public void actionPerformed(ActionEvent e)
866 showSequenceLogo_actionPerformed(e);
870 normaliseSequenceLogo
871 .setText(MessageManager.getString("label.norm_consensus_logo"));
872 normaliseSequenceLogo.addActionListener(new ActionListener()
876 public void actionPerformed(ActionEvent e)
878 normaliseSequenceLogo_actionPerformed(e);
882 applyAutoAnnotationSettings
883 .setText(MessageManager.getString("label.apply_all_groups"));
884 applyAutoAnnotationSettings.setState(false);
885 applyAutoAnnotationSettings.setVisible(true);
886 applyAutoAnnotationSettings.addActionListener(new ActionListener()
889 public void actionPerformed(ActionEvent e)
891 applyAutoAnnotationSettings_actionPerformed(e);
895 ButtonGroup buttonGroup = new ButtonGroup();
896 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
897 MessageManager.getString("label.show_first"));
898 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
899 MessageManager.getString("label.show_last"));
900 buttonGroup.add(showAutoFirst);
901 buttonGroup.add(showAutoLast);
902 final boolean autoFirst = Cache
903 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
904 showAutoFirst.setSelected(autoFirst);
905 setShowAutoCalculatedAbove(autoFirst);
906 showAutoFirst.addActionListener(new ActionListener()
909 public void actionPerformed(ActionEvent e)
911 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
912 sortAnnotations_actionPerformed();
915 showAutoLast.setSelected(!showAutoFirst.isSelected());
916 showAutoLast.addActionListener(new ActionListener()
919 public void actionPerformed(ActionEvent e)
921 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
922 sortAnnotations_actionPerformed();
926 JMenuItem deleteGroups = new JMenuItem(
927 MessageManager.getString("action.undefine_groups"));
928 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
929 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
930 al = new ActionListener()
933 public void actionPerformed(ActionEvent e)
935 deleteGroups_actionPerformed(e);
938 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
940 JMenuItem annotationColumn = new JMenuItem(
941 MessageManager.getString("action.select_by_annotation"));
942 annotationColumn.addActionListener(new ActionListener()
945 public void actionPerformed(ActionEvent e)
947 annotationColumn_actionPerformed(e);
951 JMenuItem createGroup = new JMenuItem(
952 MessageManager.getString("action.create_group"));
953 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
954 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
955 al = new ActionListener()
958 public void actionPerformed(ActionEvent e)
960 createGroup_actionPerformed(e);
963 addMenuActionAndAccelerator(keyStroke, createGroup, al);
965 JMenuItem unGroup = new JMenuItem(
966 MessageManager.getString("action.remove_group"));
967 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
968 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
969 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
971 al = new ActionListener()
974 public void actionPerformed(ActionEvent e)
976 unGroup_actionPerformed(e);
979 addMenuActionAndAccelerator(keyStroke, unGroup, al);
981 copy.setText(MessageManager.getString("action.copy"));
982 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
983 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
985 al = new ActionListener()
988 public void actionPerformed(ActionEvent e)
990 copy_actionPerformed(e);
993 addMenuActionAndAccelerator(keyStroke, copy, al);
995 cut.setText(MessageManager.getString("action.cut"));
996 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
997 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
998 al = new ActionListener()
1001 public void actionPerformed(ActionEvent e)
1003 cut_actionPerformed(e);
1006 addMenuActionAndAccelerator(keyStroke, cut, al);
1008 JMenuItem delete = new JMenuItem(
1009 MessageManager.getString("action.delete"));
1010 delete.addActionListener(new ActionListener()
1013 public void actionPerformed(ActionEvent e)
1015 delete_actionPerformed(e);
1019 pasteMenu.setText(MessageManager.getString("action.paste"));
1020 JMenuItem pasteNew = new JMenuItem(
1021 MessageManager.getString("label.to_new_alignment"));
1022 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1023 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1024 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1026 al = new ActionListener()
1029 public void actionPerformed(ActionEvent e)
1033 pasteNew_actionPerformed(e);
1034 } catch (IOException | InterruptedException e1)
1036 // TODO Auto-generated catch block
1037 e1.printStackTrace();
1041 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1043 JMenuItem pasteThis = new JMenuItem(
1044 MessageManager.getString("label.to_this_alignment"));
1045 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1046 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1047 al = new ActionListener()
1050 public void actionPerformed(ActionEvent e)
1054 pasteThis_actionPerformed(e);
1055 } catch (IOException | InterruptedException e1)
1057 // TODO Auto-generated catch block
1058 e1.printStackTrace();
1062 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1064 JMenuItem createPNG = new JMenuItem("PNG");
1065 createPNG.addActionListener(new ActionListener()
1068 public void actionPerformed(ActionEvent e)
1073 createPNG.setActionCommand(
1074 MessageManager.getString("label.save_png_image"));
1075 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1076 font.addActionListener(new ActionListener()
1079 public void actionPerformed(ActionEvent e)
1081 font_actionPerformed(e);
1085 MessageManager.getString("label.show_sequence_limits"));
1086 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1087 seqLimits.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 seqLimit_actionPerformed(e);
1095 JMenuItem epsFile = new JMenuItem("EPS");
1096 epsFile.addActionListener(new ActionListener()
1099 public void actionPerformed(ActionEvent e)
1105 JMenuItem createSVG = new JMenuItem("SVG");
1106 createSVG.addActionListener(new ActionListener()
1109 public void actionPerformed(ActionEvent e)
1115 JMenuItem loadTreeMenuItem = new JMenuItem(
1116 MessageManager.getString("label.load_associated_tree"));
1117 loadTreeMenuItem.setActionCommand(
1118 MessageManager.getString("label.load_tree_for_sequence_set"));
1119 loadTreeMenuItem.addActionListener(new ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 loadTreeMenuItem_actionPerformed(e);
1128 scaleAbove.setVisible(false);
1129 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1130 scaleAbove.addActionListener(new ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 scaleAbove_actionPerformed(e);
1138 scaleLeft.setVisible(false);
1139 scaleLeft.setSelected(true);
1140 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1141 scaleLeft.addActionListener(new ActionListener()
1144 public void actionPerformed(ActionEvent e)
1146 scaleLeft_actionPerformed(e);
1149 scaleRight.setVisible(false);
1150 scaleRight.setSelected(true);
1151 scaleRight.setText(MessageManager.getString("action.scale_right"));
1152 scaleRight.addActionListener(new ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 scaleRight_actionPerformed(e);
1160 centreColumnLabelsMenuItem.setVisible(true);
1161 centreColumnLabelsMenuItem.setState(false);
1162 centreColumnLabelsMenuItem.setText(
1163 MessageManager.getString("label.centre_column_labels"));
1164 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1167 public void actionPerformed(ActionEvent e)
1169 centreColumnLabels_actionPerformed(e);
1172 followHighlightMenuItem.setVisible(true);
1173 followHighlightMenuItem.setState(true);
1174 followHighlightMenuItem
1175 .setText(MessageManager.getString("label.automatic_scrolling"));
1176 followHighlightMenuItem.addActionListener(new ActionListener()
1180 public void actionPerformed(ActionEvent e)
1182 followHighlight_actionPerformed();
1188 .setText(MessageManager.getString("action.by_tree_order"));
1189 sort.setText(MessageManager.getString("action.sort"));
1190 sort.addMenuListener(new MenuListener()
1193 public void menuSelected(MenuEvent e)
1195 buildTreeSortMenu();
1199 public void menuDeselected(MenuEvent e)
1204 public void menuCanceled(MenuEvent e)
1209 .setText(MessageManager.getString("label.sort_by_score"));
1210 sort.add(sortByAnnotScore);
1211 sort.addMenuListener(new javax.swing.event.MenuListener()
1215 public void menuCanceled(MenuEvent e)
1220 public void menuDeselected(MenuEvent e)
1225 public void menuSelected(MenuEvent e)
1227 buildSortByAnnotationScoresMenu();
1230 sortByAnnotScore.setVisible(false);
1233 .setText(MessageManager.getString("action.calculate_tree_pca"));
1235 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1237 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1238 padGapsMenuitem.addActionListener(new ActionListener()
1241 public void actionPerformed(ActionEvent e)
1243 padGapsMenuitem_actionPerformed(e);
1246 JMenuItem vamsasStore = new JMenuItem(
1247 MessageManager.getString("label.vamsas_store"));
1248 vamsasStore.setVisible(false);
1249 vamsasStore.addActionListener(new ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 vamsasStore_actionPerformed(e);
1259 * Translate as cDNA with sub-menu of translation tables
1261 showTranslation.setText(MessageManager
1262 .getString("label.translate_cDNA"));
1263 boolean first = true;
1264 for (final GeneticCodeI table : GeneticCodes.getInstance()
1267 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1268 showTranslation.add(item);
1269 item.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 showTranslation_actionPerformed(table);
1279 showTranslation.addSeparator();
1284 showReverse.setText(MessageManager.getString("label.reverse"));
1285 showReverse.addActionListener(new ActionListener()
1288 public void actionPerformed(ActionEvent e)
1290 showReverse_actionPerformed(false);
1293 showReverseComplement
1294 .setText(MessageManager.getString("label.reverse_complement"));
1295 showReverseComplement.addActionListener(new ActionListener()
1298 public void actionPerformed(ActionEvent e)
1300 showReverse_actionPerformed(true);
1304 JMenuItem extractScores = new JMenuItem(
1305 MessageManager.getString("label.extract_scores"));
1306 extractScores.addActionListener(new ActionListener()
1309 public void actionPerformed(ActionEvent e)
1311 extractScores_actionPerformed(e);
1314 extractScores.setVisible(true);
1315 // JBPNote: TODO: make gui for regex based score extraction
1317 // for show products actions see AlignFrame.canShowProducts
1318 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1320 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1321 runGroovy.setToolTipText(
1322 MessageManager.getString("label.run_groovy_tip"));
1323 runGroovy.addActionListener(new ActionListener()
1326 public void actionPerformed(ActionEvent e)
1328 runGroovy_actionPerformed();
1332 JMenuItem openFeatureSettings = new JMenuItem(
1333 MessageManager.getString("action.feature_settings"));
1334 openFeatureSettings.addActionListener(new ActionListener()
1337 public void actionPerformed(ActionEvent e)
1339 featureSettings_actionPerformed(e);
1342 JMenuItem fetchSequence = new JMenuItem(
1343 MessageManager.getString("label.fetch_sequences"));
1344 fetchSequence.addActionListener(new ActionListener()
1347 public void actionPerformed(ActionEvent e)
1349 fetchSequence_actionPerformed(e);
1353 JMenuItem associatedData = new JMenuItem(
1354 MessageManager.getString("label.load_features_annotations"));
1355 associatedData.addActionListener(new ActionListener()
1358 public void actionPerformed(ActionEvent e)
1362 associatedData_actionPerformed(e);
1363 } catch (IOException | InterruptedException e1)
1365 // TODO Auto-generated catch block
1366 e1.printStackTrace();
1370 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1371 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1372 loadVcf.addActionListener(new ActionListener()
1375 public void actionPerformed(ActionEvent e)
1377 loadVcf_actionPerformed();
1380 autoCalculate.setText(
1381 MessageManager.getString("label.autocalculate_consensus"));
1382 autoCalculate.setState(
1383 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1384 autoCalculate.addActionListener(new ActionListener()
1387 public void actionPerformed(ActionEvent e)
1389 autoCalculate_actionPerformed(e);
1393 MessageManager.getString("label.sort_alignment_new_tree"));
1394 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1395 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1397 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1398 sortByTree.addActionListener(new ActionListener()
1401 public void actionPerformed(ActionEvent e)
1403 sortByTreeOption_actionPerformed(e);
1407 listenToViewSelections.setText(
1408 MessageManager.getString("label.listen_for_selections"));
1409 listenToViewSelections
1410 .setToolTipText("<html>" + MessageManager.getString(
1411 "label.selections_mirror_selections_made_same_sequences_other_views"));
1412 listenToViewSelections.setState(false);
1413 listenToViewSelections.addActionListener(new ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 listenToViewSelections_actionPerformed(e);
1422 JMenu addSequenceMenu = new JMenu(
1423 MessageManager.getString("label.add_sequences"));
1424 JMenuItem addFromFile = new JMenuItem(
1425 MessageManager.getString("label.from_file"));
1426 addFromFile.addActionListener(new ActionListener()
1429 public void actionPerformed(ActionEvent e)
1431 addFromFile_actionPerformed(e);
1434 JMenuItem addFromText = new JMenuItem(
1435 MessageManager.getString("label.from_textbox"));
1436 addFromText.addActionListener(new ActionListener()
1439 public void actionPerformed(ActionEvent e)
1441 addFromText_actionPerformed(e);
1444 JMenuItem addFromURL = new JMenuItem(
1445 MessageManager.getString("label.from_url"));
1446 addFromURL.addActionListener(new ActionListener()
1449 public void actionPerformed(ActionEvent e)
1451 addFromURL_actionPerformed(e);
1454 JMenuItem exportFeatures = new JMenuItem(
1455 MessageManager.getString("label.export_features"));
1456 exportFeatures.addActionListener(new ActionListener()
1459 public void actionPerformed(ActionEvent e)
1461 exportFeatures_actionPerformed(e);
1464 JMenuItem exportAnnotations = new JMenuItem(
1465 MessageManager.getString("label.export_annotations"));
1466 exportAnnotations.addActionListener(new ActionListener()
1469 public void actionPerformed(ActionEvent e)
1471 exportAnnotations_actionPerformed(e);
1474 statusPanel.setLayout(new GridLayout());
1475 JMenuItem showAllSeqs = new JMenuItem(
1476 MessageManager.getString("label.all_sequences"));
1477 showAllSeqs.setToolTipText(
1478 MessageManager.getString("label.toggle_sequence_visibility"));
1479 showAllSeqs.addActionListener(new ActionListener()
1482 public void actionPerformed(ActionEvent e)
1484 showAllSeqs_actionPerformed(e);
1487 JMenuItem showAllColumns = new JMenuItem(
1488 MessageManager.getString("label.all_columns"));
1489 showAllColumns.setToolTipText(
1490 MessageManager.getString("label.toggle_columns_visibility"));
1491 showAllColumns.addActionListener(new ActionListener()
1494 public void actionPerformed(ActionEvent e)
1496 showAllColumns_actionPerformed(e);
1499 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1500 JMenuItem hideSelSequences = new JMenuItem(
1501 MessageManager.getString("label.selected_sequences"));
1502 hideSelSequences.setToolTipText(
1503 MessageManager.getString("label.toggle_sequence_visibility"));
1504 hideSelSequences.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 hideSelSequences_actionPerformed(e);
1512 JMenuItem hideSelColumns = new JMenuItem(
1513 MessageManager.getString("label.selected_columns"));
1514 hideSelColumns.setToolTipText(
1515 MessageManager.getString("label.toggle_columns_visibility"));
1516 hideSelColumns.addActionListener(new ActionListener()
1519 public void actionPerformed(ActionEvent e)
1521 hideSelColumns_actionPerformed(e);
1524 JMenuItem hideAllSelection = new JMenuItem(
1525 MessageManager.getString("label.selected_region"));
1526 hideAllSelection.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 hideAllSelection_actionPerformed(e);
1534 // TODO: should be hidden if no selection exists.
1535 JMenuItem hideAllButSelection = new JMenuItem(
1536 MessageManager.getString("label.all_but_selected_region"));
1537 hideAllButSelection.addActionListener(new ActionListener()
1540 public void actionPerformed(ActionEvent e)
1542 hideAllButSelection_actionPerformed(e);
1545 JMenuItem showAllhidden = new JMenuItem(
1546 MessageManager.getString("label.all_sequences_columns"));
1547 showAllhidden.setToolTipText(MessageManager
1548 .getString("label.toggles_visibility_hidden_selected_regions"));
1549 showAllhidden.addActionListener(new ActionListener()
1552 public void actionPerformed(ActionEvent e)
1554 showAllhidden_actionPerformed(e);
1557 hiddenMarkers.setText(
1558 MessageManager.getString("action.show_hidden_markers"));
1559 hiddenMarkers.addActionListener(new ActionListener()
1562 public void actionPerformed(ActionEvent e)
1564 hiddenMarkers_actionPerformed(e);
1568 JMenuItem invertColSel = new JMenuItem(
1569 MessageManager.getString("action.invert_column_selection"));
1570 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1571 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1572 | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1574 al = new ActionListener()
1577 public void actionPerformed(ActionEvent e)
1579 invertColSel_actionPerformed(e);
1582 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1584 showComplementMenuItem.setVisible(false);
1585 showComplementMenuItem.addActionListener(new ActionListener()
1588 public void actionPerformed(ActionEvent e)
1590 showComplement_actionPerformed(showComplementMenuItem.getState());
1594 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1597 public void stateChanged(ChangeEvent evt)
1599 JTabbedPane pane = (JTabbedPane) evt.getSource();
1600 int sel = pane.getSelectedIndex();
1601 tabSelectionChanged(sel);
1604 tabbedPane.addMouseListener(new MouseAdapter()
1607 public void mousePressed(MouseEvent e)
1609 if (e.isPopupTrigger()) // Mac
1611 tabbedPane_mousePressed(e);
1616 public void mouseReleased(MouseEvent e)
1618 if (e.isPopupTrigger()) // Windows
1620 tabbedPane_mousePressed(e);
1624 tabbedPane.addFocusListener(new FocusAdapter()
1627 public void focusGained(FocusEvent e)
1629 tabbedPane_focusGained(e);
1633 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1634 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1635 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1636 al = new ActionListener()
1639 public void actionPerformed(ActionEvent e)
1641 save_actionPerformed(e);
1644 addMenuActionAndAccelerator(keyStroke, save, al);
1646 reload.setEnabled(false);
1647 reload.setText(MessageManager.getString("action.reload"));
1648 reload.addActionListener(new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 reload_actionPerformed(e);
1657 JMenuItem newView = new JMenuItem(
1658 MessageManager.getString("action.new_view"));
1659 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1660 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
1661 al = new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 newView_actionPerformed(e);
1669 addMenuActionAndAccelerator(keyStroke, newView, al);
1671 tabbedPane.setToolTipText("<html><i>"
1672 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1675 formatMenu.setText(MessageManager.getString("action.format"));
1676 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1678 idRightAlign.setText(
1679 MessageManager.getString("label.right_align_sequence_id"));
1680 idRightAlign.addActionListener(new ActionListener()
1683 public void actionPerformed(ActionEvent e)
1685 idRightAlign_actionPerformed(e);
1689 gatherViews.setEnabled(false);
1690 gatherViews.setText(MessageManager.getString("action.gather_views"));
1691 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1692 al = new ActionListener()
1695 public void actionPerformed(ActionEvent e)
1697 gatherViews_actionPerformed(e);
1700 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1702 expandViews.setEnabled(false);
1703 expandViews.setText(MessageManager.getString("action.expand_views"));
1704 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1705 al = new ActionListener()
1708 public void actionPerformed(ActionEvent e)
1710 expandViews_actionPerformed(e);
1713 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1715 JMenuItem pageSetup = new JMenuItem(
1716 MessageManager.getString("action.page_setup"));
1717 pageSetup.addActionListener(new ActionListener()
1720 public void actionPerformed(ActionEvent e)
1722 pageSetup_actionPerformed(e);
1725 JMenuItem alignmentProperties = new JMenuItem(
1726 MessageManager.getString("label.alignment_props"));
1727 alignmentProperties.addActionListener(new ActionListener()
1730 public void actionPerformed(ActionEvent actionEvent)
1732 alignmentProperties();
1735 JMenuItem selectHighlighted = new JMenuItem(
1736 MessageManager.getString("action.select_highlighted_columns"));
1737 selectHighlighted.setToolTipText(
1738 MessageManager.getString("tooltip.select_highlighted_columns"));
1739 al = new ActionListener()
1742 public void actionPerformed(ActionEvent actionEvent)
1744 selectHighlightedColumns_actionPerformed(actionEvent);
1747 selectHighlighted.addActionListener(al);
1748 JMenu tooltipSettingsMenu = new JMenu(
1749 MessageManager.getString("label.sequence_id_tooltip"));
1750 JMenu autoAnnMenu = new JMenu(
1751 MessageManager.getString("label.autocalculated_annotation"));
1753 JMenu exportImageMenu = new JMenu(
1754 MessageManager.getString("label.export_image"));
1755 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1756 alignFrameMenuBar.add(fileMenu);
1757 alignFrameMenuBar.add(editMenu);
1758 alignFrameMenuBar.add(selectMenu);
1759 alignFrameMenuBar.add(viewMenu);
1760 alignFrameMenuBar.add(annotationsMenu);
1761 alignFrameMenuBar.add(formatMenu);
1762 alignFrameMenuBar.add(colourMenu);
1763 alignFrameMenuBar.add(calculateMenu);
1764 alignFrameMenuBar.add(webService);
1765 alignFrameMenuBar.add(hmmerMenu);
1767 fileMenu.add(fetchSequence);
1768 fileMenu.add(addSequenceMenu);
1769 fileMenu.add(reload);
1770 fileMenu.addSeparator();
1771 fileMenu.add(vamsasStore);
1773 fileMenu.add(saveAs);
1774 fileMenu.add(outputTextboxMenu);
1775 fileMenu.add(pageSetup);
1776 fileMenu.add(printMenuItem);
1777 fileMenu.addSeparator();
1778 fileMenu.add(exportImageMenu);
1779 fileMenu.add(exportFeatures);
1780 fileMenu.add(exportAnnotations);
1781 fileMenu.add(loadTreeMenuItem);
1782 fileMenu.add(associatedData);
1783 fileMenu.add(loadVcf);
1784 fileMenu.addSeparator();
1785 fileMenu.add(closeMenuItem);
1787 pasteMenu.add(pasteNew);
1788 pasteMenu.add(pasteThis);
1789 editMenu.add(undoMenuItem);
1790 editMenu.add(redoMenuItem);
1793 editMenu.add(pasteMenu);
1794 editMenu.add(delete);
1795 editMenu.addSeparator();
1796 editMenu.add(remove2LeftMenuItem);
1797 editMenu.add(remove2RightMenuItem);
1798 editMenu.add(removeGappedColumnMenuItem);
1799 editMenu.add(removeAllGapsMenuItem);
1800 editMenu.add(removeRedundancyMenuItem);
1801 editMenu.addSeparator();
1802 // dont add these yet in the CVS build - they cannot be undone!
1803 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1804 // editMenu.add(justifyLeftMenuItem);
1805 // editMenu.add(justifyRightMenuItem);
1806 // editMenu.addSeparator();
1807 editMenu.add(padGapsMenuitem);
1809 showMenu.add(showAllColumns);
1810 showMenu.add(showAllSeqs);
1811 showMenu.add(showAllhidden);
1812 hideMenu.add(hideSelColumns);
1813 hideMenu.add(hideSelSequences);
1814 hideMenu.add(hideAllSelection);
1815 hideMenu.add(hideAllButSelection);
1816 viewMenu.add(newView);
1817 viewMenu.add(expandViews);
1818 viewMenu.add(gatherViews);
1819 viewMenu.addSeparator();
1820 viewMenu.add(showMenu);
1821 viewMenu.add(hideMenu);
1822 viewMenu.add(showComplementMenuItem);
1823 viewMenu.addSeparator();
1824 viewMenu.add(followHighlightMenuItem);
1825 viewMenu.addSeparator();
1826 viewMenu.add(showSeqFeatures);
1827 // viewMenu.add(showSeqFeaturesHeight);
1828 viewMenu.add(openFeatureSettings);
1829 tooltipSettingsMenu.add(showDbRefsMenuitem);
1830 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1831 viewMenu.add(tooltipSettingsMenu);
1832 viewMenu.addSeparator();
1833 viewMenu.add(alignmentProperties);
1834 viewMenu.addSeparator();
1835 viewMenu.add(overviewMenuItem);
1837 annotationsMenu.add(annotationPanelMenuItem);
1838 annotationsMenu.addSeparator();
1839 annotationsMenu.add(showAllAlAnnotations);
1840 annotationsMenu.add(hideAllAlAnnotations);
1841 annotationsMenu.addSeparator();
1842 annotationsMenu.add(showAllSeqAnnotations);
1843 annotationsMenu.add(hideAllSeqAnnotations);
1844 annotationsMenu.add(sortAnnBySequence);
1845 annotationsMenu.add(sortAnnByLabel);
1846 annotationsMenu.addSeparator();
1847 autoAnnMenu.add(showAutoFirst);
1848 autoAnnMenu.add(showAutoLast);
1849 autoAnnMenu.addSeparator();
1850 autoAnnMenu.add(applyAutoAnnotationSettings);
1851 autoAnnMenu.add(showConsensusHistogram);
1852 autoAnnMenu.add(showSequenceLogo);
1853 autoAnnMenu.add(normaliseSequenceLogo);
1854 autoAnnMenu.addSeparator();
1855 autoAnnMenu.add(showGroupConservation);
1856 autoAnnMenu.add(showGroupConsensus);
1857 annotationsMenu.add(autoAnnMenu);
1859 sort.add(sortIDMenuItem);
1860 sort.add(sortLengthMenuItem);
1861 sort.add(sortGroupMenuItem);
1862 sort.add(sortPairwiseMenuItem);
1863 sort.add(sortByTreeMenu);
1864 calculateMenu.add(sort);
1865 calculateMenu.add(calculateTree);
1866 calculateMenu.addSeparator();
1867 calculateMenu.add(pairwiseAlignmentMenuItem);
1868 calculateMenu.addSeparator();
1869 calculateMenu.add(showTranslation);
1870 calculateMenu.add(showReverse);
1871 calculateMenu.add(showReverseComplement);
1872 calculateMenu.add(showProducts);
1873 calculateMenu.add(autoCalculate);
1874 calculateMenu.add(sortByTree);
1875 calculateMenu.addSeparator();
1876 calculateMenu.add(expandAlignment);
1877 calculateMenu.add(extractScores);
1878 calculateMenu.addSeparator();
1879 calculateMenu.add(runGroovy);
1881 webServiceNoServices = new JMenuItem(
1882 MessageManager.getString("label.no_services"));
1883 webService.add(webServiceNoServices);
1884 exportImageMenu.add(htmlMenuItem);
1885 exportImageMenu.add(epsFile);
1886 exportImageMenu.add(createPNG);
1887 exportImageMenu.add(createBioJS);
1888 exportImageMenu.add(createSVG);
1889 addSequenceMenu.add(addFromFile);
1890 addSequenceMenu.add(addFromText);
1891 addSequenceMenu.add(addFromURL);
1892 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1893 statusPanel.add(statusBar, null);
1894 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1896 formatMenu.add(font);
1897 formatMenu.addSeparator();
1898 formatMenu.add(wrapMenuItem);
1899 formatMenu.add(scaleAbove);
1900 formatMenu.add(scaleLeft);
1901 formatMenu.add(scaleRight);
1902 formatMenu.add(seqLimits);
1903 formatMenu.add(idRightAlign);
1904 formatMenu.add(hiddenMarkers);
1905 formatMenu.add(viewBoxesMenuItem);
1906 formatMenu.add(viewTextMenuItem);
1907 formatMenu.add(colourTextMenuItem);
1908 formatMenu.add(renderGapsMenuItem);
1909 formatMenu.add(centreColumnLabelsMenuItem);
1910 formatMenu.add(showNonconservedMenuItem);
1911 selectMenu.add(findMenuItem);
1912 selectMenu.addSeparator();
1913 selectMenu.add(selectAllSequenceMenuItem);
1914 selectMenu.add(deselectAllSequenceMenuItem);
1915 selectMenu.add(invertSequenceMenuItem);
1916 selectMenu.add(invertColSel);
1917 selectMenu.add(createGroup);
1918 selectMenu.add(unGroup);
1919 selectMenu.add(grpsFromSelection);
1920 selectMenu.add(deleteGroups);
1921 selectMenu.add(annotationColumn);
1922 selectMenu.add(selectHighlighted);
1923 // TODO - determine if the listenToViewSelections button is needed : see bug
1925 // selectMenu.addSeparator();
1926 // selectMenu.add(listenToViewSelections);
1930 * Constructs the entries on the HMMER menu
1932 protected void initHMMERMenu()
1937 JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
1938 JMenuItem hmmBuildSettings = new JMenuItem(
1939 MessageManager.getString("label.edit_settings_and_run"));
1940 hmmBuildSettings.addActionListener(new ActionListener()
1943 public void actionPerformed(ActionEvent e)
1945 hmmBuild_actionPerformed(false);
1948 JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
1949 "label.action_with_default_settings", "hmmbuild"));
1950 hmmBuildRun.addActionListener(new ActionListener()
1953 public void actionPerformed(ActionEvent e)
1955 hmmBuild_actionPerformed(true);
1958 hmmBuild.add(hmmBuildRun);
1959 hmmBuild.add(hmmBuildSettings);
1964 JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
1965 JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
1966 "label.action_with_default_settings", "hmmalign"));
1967 hmmAlignRun.addActionListener(new ActionListener()
1970 public void actionPerformed(ActionEvent e)
1972 hmmAlign_actionPerformed(true);
1975 JMenuItem hmmAlignSettings = new JMenuItem(
1976 MessageManager.getString("label.edit_settings_and_run"));
1977 hmmAlignSettings.addActionListener(new ActionListener()
1980 public void actionPerformed(ActionEvent e)
1982 hmmAlign_actionPerformed(false);
1985 hmmAlign.add(hmmAlignRun);
1986 hmmAlign.add(hmmAlignSettings);
1991 JMenu hmmSearch = new JMenu(
1992 MessageManager.getString("label.hmmsearch"));
1993 JMenuItem hmmSearchSettings = new JMenuItem(
1994 MessageManager.getString("label.edit_settings_and_run"));
1995 hmmSearchSettings.addActionListener(new ActionListener()
1998 public void actionPerformed(ActionEvent e)
2000 hmmSearch_actionPerformed(false);
2003 JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
2004 "label.action_with_default_settings", "hmmsearch"));
2005 hmmSearchRun.addActionListener(new ActionListener()
2008 public void actionPerformed(ActionEvent e)
2010 hmmSearch_actionPerformed(true);
2013 JMenuItem addDatabase = new JMenuItem(
2014 MessageManager.getString("label.add_database"));
2015 addDatabase.addActionListener(new ActionListener()
2018 public void actionPerformed(ActionEvent e)
2022 addDatabase_actionPerformed();
2023 } catch (IOException e1)
2025 e1.printStackTrace();
2029 hmmSearch.add(hmmSearchRun);
2030 hmmSearch.add(hmmSearchSettings);
2031 // hmmSearch.add(addDatabase);
2036 hmmerMenu.setText(MessageManager.getString("action.hmmer"));
2037 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
2038 hmmerMenu.add(hmmBuild);
2039 hmmerMenu.add(hmmAlign);
2040 hmmerMenu.add(hmmSearch);
2044 protected void loadVcf_actionPerformed()
2049 * Constructs the entries on the Colour menu (but does not add them to the
2052 protected void initColourMenu()
2054 applyToAllGroups = new JCheckBoxMenuItem(
2055 MessageManager.getString("label.apply_colour_to_all_groups"));
2056 applyToAllGroups.addActionListener(new ActionListener()
2059 public void actionPerformed(ActionEvent e)
2061 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2065 textColour = new JMenuItem(
2066 MessageManager.getString("label.text_colour"));
2067 textColour.addActionListener(new ActionListener()
2070 public void actionPerformed(ActionEvent e)
2072 textColour_actionPerformed();
2076 conservationMenuItem = new JCheckBoxMenuItem(
2077 MessageManager.getString("action.by_conservation"));
2078 conservationMenuItem.addActionListener(new ActionListener()
2081 public void actionPerformed(ActionEvent e)
2083 conservationMenuItem_actionPerformed(
2084 conservationMenuItem.isSelected());
2088 abovePIDThreshold = new JCheckBoxMenuItem(
2089 MessageManager.getString("label.above_identity_threshold"));
2090 abovePIDThreshold.addActionListener(new ActionListener()
2093 public void actionPerformed(ActionEvent e)
2095 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2098 modifyPID = new JMenuItem(
2099 MessageManager.getString("label.modify_identity_threshold"));
2100 modifyPID.addActionListener(new ActionListener()
2103 public void actionPerformed(ActionEvent e)
2105 modifyPID_actionPerformed();
2108 modifyConservation = new JMenuItem(MessageManager
2109 .getString("label.modify_conservation_threshold"));
2110 modifyConservation.addActionListener(new ActionListener()
2113 public void actionPerformed(ActionEvent e)
2115 modifyConservation_actionPerformed();
2119 annotationColour = new JRadioButtonMenuItem(
2120 MessageManager.getString("action.by_annotation"));
2121 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2122 annotationColour.addActionListener(new ActionListener()
2125 public void actionPerformed(ActionEvent e)
2127 annotationColour_actionPerformed();
2132 protected void selectHighlightedColumns_actionPerformed(
2133 ActionEvent actionEvent)
2135 // TODO Auto-generated method stub
2140 * Generate the reverse sequence (or reverse complement if the flag is true)
2141 * and add it to the alignment
2145 protected void showReverse_actionPerformed(boolean complement)
2150 * Try to run script in a Groovy console, having first ensured that this
2151 * alignframe is set as currentAlignFrame in Desktop
2153 protected void runGroovy_actionPerformed()
2159 * Adds the given action listener and key accelerator to the given menu item.
2160 * Also saves in a lookup table to support lookup of action by key stroke.
2164 * @param actionListener
2166 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2167 JMenuItem menuItem, ActionListener actionListener)
2169 menuItem.setAccelerator(keyStroke);
2170 accelerators.put(keyStroke, menuItem);
2171 menuItem.addActionListener(actionListener);
2175 * Action on clicking sort annotations by type.
2179 protected void sortAnnotations_actionPerformed()
2184 * Action on clicking Show all annotations.
2186 * @param forSequences
2187 * update sequence-related annotations
2188 * @param forAlignment
2189 * update non-sequence-related annotations
2191 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2192 boolean forAlignment)
2194 setAnnotationsVisibility(true, forSequences, forAlignment);
2198 * Action on clicking Hide all annotations.
2200 * @param forSequences
2201 * update sequence-related annotations
2202 * @param forAlignment
2203 * update non-sequence-related annotations
2205 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2206 boolean forAlignment)
2208 setAnnotationsVisibility(false, forSequences, forAlignment);
2212 * Set the visibility of annotations to true or false. Can act on
2213 * sequence-related annotations, or alignment-related, or both.
2216 * @param forSequences
2217 * update sequence-related annotations
2218 * @param forAlignment
2219 * update non-sequence-related annotations
2221 protected void setAnnotationsVisibility(boolean visible,
2222 boolean forSequences, boolean forAlignment)
2227 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2229 // TODO Auto-generated method stub
2233 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2235 // TODO Auto-generated method stub
2239 protected void showAllhidden_actionPerformed(ActionEvent e)
2241 // TODO Auto-generated method stub
2245 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2247 // TODO Auto-generated method stub
2251 protected void hideAllSelection_actionPerformed(ActionEvent e)
2253 // TODO Auto-generated method stub
2257 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2259 // TODO Auto-generated method stub
2263 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2265 // TODO Auto-generated method stub
2269 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2271 // TODO Auto-generated method stub
2275 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2277 // TODO Auto-generated method stub
2281 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2283 // TODO Auto-generated method stub
2287 protected void showGroupConservation_actionPerformed(ActionEvent e)
2289 // TODO Auto-generated method stub
2293 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2295 // TODO Auto-generated method stub
2299 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2301 // TODO Auto-generated method stub
2305 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2307 // TODO Auto-generated method stub
2311 protected void followHighlight_actionPerformed()
2313 // TODO Auto-generated method stub
2317 protected void showNpFeats_actionPerformed(ActionEvent e)
2319 // TODO Auto-generated method stub
2323 protected void showDbRefs_actionPerformed(ActionEvent e)
2325 // TODO Auto-generated method stub
2329 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2333 protected void buildSortByAnnotationScoresMenu()
2337 protected void extractScores_actionPerformed(ActionEvent e)
2341 protected void outputText_actionPerformed(ActionEvent e)
2345 public void addFromFile_actionPerformed(ActionEvent e)
2350 public void addFromText_actionPerformed(ActionEvent e)
2355 public void addFromURL_actionPerformed(ActionEvent e)
2360 public void exportFeatures_actionPerformed(ActionEvent e)
2365 public void exportAnnotations_actionPerformed(ActionEvent e)
2370 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2374 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2379 protected void closeMenuItem_actionPerformed(boolean b)
2383 protected void redoMenuItem_actionPerformed(ActionEvent e)
2387 protected void undoMenuItem_actionPerformed(ActionEvent e)
2391 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2395 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2399 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2403 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2407 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2411 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2415 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2419 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2423 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2427 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2431 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2435 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2439 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2443 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2447 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2451 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2455 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2459 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2463 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2467 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2471 protected void conservationMenuItem_actionPerformed(boolean selected)
2475 protected void printMenuItem_actionPerformed(ActionEvent e)
2479 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2483 protected void findMenuItem_actionPerformed(ActionEvent e)
2487 protected void abovePIDThreshold_actionPerformed(boolean selected)
2491 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2495 protected void deleteGroups_actionPerformed(ActionEvent e)
2499 protected void createGroup_actionPerformed(ActionEvent e)
2503 protected void unGroup_actionPerformed(ActionEvent e)
2507 protected void copy_actionPerformed(ActionEvent e)
2511 protected void cut_actionPerformed(ActionEvent e)
2515 protected void delete_actionPerformed(ActionEvent e)
2519 protected void pasteNew_actionPerformed(ActionEvent e)
2520 throws IOException, InterruptedException
2524 protected void pasteThis_actionPerformed(ActionEvent e)
2525 throws IOException, InterruptedException
2529 protected void applyToAllGroups_actionPerformed(boolean selected)
2533 protected void hmmBuild_actionPerformed(boolean withDefaults)
2537 protected void hmmSearch_actionPerformed(boolean withDefaults)
2541 protected void addDatabase_actionPerformed()
2542 throws FileFormatException, IOException
2546 protected void hmmAlign_actionPerformed(boolean withDefaults)
2550 public void createPNG(java.io.File f)
2554 protected void font_actionPerformed(ActionEvent e)
2558 protected void seqLimit_actionPerformed(ActionEvent e)
2562 public void seqDBRef_actionPerformed(ActionEvent e)
2567 public void createEPS(java.io.File f)
2571 public void createSVG(java.io.File f)
2576 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2582 * Template method to handle the 'load T-Coffee scores' menu event.
2584 * Subclasses override this method to provide a custom action.
2589 protected void loadScores_actionPerformed(ActionEvent event)
2594 protected void jpred_actionPerformed(ActionEvent e)
2598 protected void scaleAbove_actionPerformed(ActionEvent e)
2602 protected void scaleLeft_actionPerformed(ActionEvent e)
2606 protected void scaleRight_actionPerformed(ActionEvent e)
2610 protected void modifyPID_actionPerformed()
2614 protected void modifyConservation_actionPerformed()
2618 protected void saveAs_actionPerformed(ActionEvent e)
2622 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2626 public void vamsasStore_actionPerformed(ActionEvent e)
2631 public void vamsasLoad_actionPerformed(ActionEvent e)
2636 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2641 public void featureSettings_actionPerformed(ActionEvent e)
2646 public void fetchSequence_actionPerformed(ActionEvent e)
2651 public void smoothFont_actionPerformed(ActionEvent e)
2656 public void annotationColour_actionPerformed()
2660 public void annotationColumn_actionPerformed(ActionEvent e)
2664 public void associatedData_actionPerformed(ActionEvent e)
2665 throws IOException, InterruptedException
2670 public void autoCalculate_actionPerformed(ActionEvent e)
2675 public void sortByTreeOption_actionPerformed(ActionEvent e)
2680 public void showAllSeqs_actionPerformed(ActionEvent e)
2685 public void showAllColumns_actionPerformed(ActionEvent e)
2690 public void hideSelSequences_actionPerformed(ActionEvent e)
2695 public void hideSelColumns_actionPerformed(ActionEvent e)
2700 public void hiddenMarkers_actionPerformed(ActionEvent e)
2705 public void findPdbId_actionPerformed(ActionEvent e)
2710 public void enterPdbId_actionPerformed(ActionEvent e)
2715 public void pdbFile_actionPerformed(ActionEvent e)
2720 public void invertColSel_actionPerformed(ActionEvent e)
2725 public void tabSelectionChanged(int sel)
2730 public void tabbedPane_mousePressed(MouseEvent e)
2735 public void tabbedPane_focusGained(FocusEvent e)
2740 public void save_actionPerformed(ActionEvent e)
2745 public void reload_actionPerformed(ActionEvent e)
2750 public void newView_actionPerformed(ActionEvent e)
2755 public void textColour_actionPerformed()
2760 public void idRightAlign_actionPerformed(ActionEvent e)
2765 public void expandViews_actionPerformed(ActionEvent e)
2770 public void gatherViews_actionPerformed(ActionEvent e)
2775 public void buildTreeSortMenu()
2780 public void pageSetup_actionPerformed(ActionEvent e)
2785 public void alignmentProperties()
2790 protected void expand_newalign(ActionEvent e)
2792 // TODO Auto-generated method stub
2796 protected boolean isShowAutoCalculatedAbove()
2798 return showAutoCalculatedAbove;
2801 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2803 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2806 protected SequenceAnnotationOrder getAnnotationSortOrder()
2808 return annotationSortOrder;
2811 protected void setAnnotationSortOrder(
2812 SequenceAnnotationOrder annotationSortOrder)
2814 this.annotationSortOrder = annotationSortOrder;
2817 public Map<KeyStroke, JMenuItem> getAccelerators()
2819 return this.accelerators;
2823 * Returns the selected index of the tabbed pane, or -1 if none selected
2824 * (including the case where the tabbed pane has not been made visible).
2828 public int getTabIndex()
2830 return tabbedPane.getSelectedIndex();
2833 public JPanel getStatusPanel()
2839 * Sets a reference to the containing split frame. Also makes the 'toggle
2840 * split view' menu item visible and checked.
2844 public void setSplitFrame(SplitContainerI sf)
2846 this.splitFrame = sf;
2849 this.showComplementMenuItem.setVisible(true);
2850 this.showComplementMenuItem.setState(true);
2854 public SplitContainerI getSplitViewContainer()
2856 return this.splitFrame;
2859 protected void showComplement_actionPerformed(boolean complement)