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 java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.GridLayout;
26 import java.awt.event.ActionEvent;
27 import java.awt.event.ActionListener;
28 import java.awt.event.FocusAdapter;
29 import java.awt.event.FocusEvent;
30 import java.awt.event.KeyEvent;
31 import java.awt.event.MouseAdapter;
32 import java.awt.event.MouseEvent;
33 import java.util.HashMap;
36 import javax.swing.BorderFactory;
37 import javax.swing.ButtonGroup;
38 import javax.swing.JCheckBoxMenuItem;
39 import javax.swing.JInternalFrame;
40 import javax.swing.JLabel;
41 import javax.swing.JMenu;
42 import javax.swing.JMenuBar;
43 import javax.swing.JMenuItem;
44 import javax.swing.JPanel;
45 import javax.swing.JRadioButtonMenuItem;
46 import javax.swing.JTabbedPane;
47 import javax.swing.KeyStroke;
48 import javax.swing.event.ChangeEvent;
49 import javax.swing.event.MenuEvent;
50 import javax.swing.event.MenuListener;
52 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
53 import jalview.analysis.GeneticCodeI;
54 import jalview.analysis.GeneticCodes;
55 import jalview.api.SplitContainerI;
56 import jalview.bin.Cache;
57 import jalview.gui.JvSwingUtils;
58 import jalview.gui.Preferences;
59 import jalview.io.FileFormats;
60 import jalview.schemes.ResidueColourScheme;
61 import jalview.util.MessageManager;
62 import jalview.util.Platform;
64 @SuppressWarnings("serial")
65 public class GAlignFrame extends JInternalFrame
67 protected JMenuBar alignFrameMenuBar = new JMenuBar();
69 protected JMenuItem closeMenuItem = new JMenuItem();
71 public JMenu webService = new JMenu();// BH 2019 was protected, but not
72 // sufficient for AlignFrame thread run
74 public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
75 // sufficient for AlignFrame thread run
77 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
79 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
81 protected JMenu sortByAnnotScore = new JMenu();
83 public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
85 // AlignFrame.printWriter
87 protected JMenu outputTextboxMenu = new JMenu();
89 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
91 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
93 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
95 protected JMenuItem undoMenuItem = new JMenuItem();
97 protected JMenuItem redoMenuItem = new JMenuItem();
99 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
101 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
103 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
105 JMenuItem copy = new JMenuItem();
107 JMenuItem copyHighlighted = new JMenuItem();
109 JMenuItem cut = new JMenuItem();
111 JMenu pasteMenu = new JMenu();
113 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
115 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
117 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
119 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
121 protected JCheckBoxMenuItem applyToAllGroups;
123 protected JMenu colourMenu = new JMenu();
125 protected JMenuItem textColour;
127 protected JCheckBoxMenuItem conservationMenuItem;
129 protected JMenuItem modifyConservation;
131 protected JCheckBoxMenuItem abovePIDThreshold;
133 protected JMenuItem modifyPID;
135 protected JRadioButtonMenuItem annotationColour;
137 protected JMenu sortByTreeMenu = new JMenu();
139 protected JMenu sort = new JMenu();
141 protected JMenuItem calculateTree = new JMenuItem();
143 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
145 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
147 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
149 protected JMenu showTranslation = new JMenu();
151 protected JMenuItem showReverse = new JMenuItem();
153 protected JMenuItem showReverseComplement = new JMenuItem();
155 protected JMenu showProducts = new JMenu();
157 protected JMenuItem runGroovy = new JMenuItem();
159 protected JMenuItem loadVcf;
161 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
163 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
165 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
167 protected JPanel statusPanel = new JPanel();
169 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
171 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
173 protected JMenuItem showAllAlAnnotations = new JMenuItem();
175 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
177 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
179 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
181 protected JTabbedPane tabbedPane = new JTabbedPane();
183 protected JMenuItem reload = new JMenuItem();
185 protected JMenu formatMenu = new JMenu();
187 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
189 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
191 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
193 protected JMenuItem gatherViews = new JMenuItem();
195 protected JMenuItem expandViews = new JMenuItem();
197 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
203 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
209 protected JMenuItem openFeatureSettings;
211 private SequenceAnnotationOrder annotationSortOrder;
213 private boolean showAutoCalculatedAbove = false;
215 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
217 private SplitContainerI splitFrame;
225 // for Web-page embedding using id=align-frame-div
226 setName("jalview-alignment");
229 setJMenuBar(alignFrameMenuBar);
231 // dynamically fill save as menu with available formats
232 for (String ff : FileFormats.getInstance().getWritableFormats(true))
234 JMenuItem item = new JMenuItem(ff);
236 item.addActionListener(new ActionListener()
239 public void actionPerformed(ActionEvent e)
241 outputText_actionPerformed(e.getActionCommand());
245 outputTextboxMenu.add(item);
247 } catch (Exception e)
249 jalview.bin.Console.errPrintln(e.toString());
252 if (Platform.allowMnemonics()) // was "not mac and not JS"
254 closeMenuItem.setMnemonic('C');
255 outputTextboxMenu.setMnemonic('T');
256 undoMenuItem.setMnemonic('Z');
257 redoMenuItem.setMnemonic('0');
258 copy.setMnemonic('C');
259 cut.setMnemonic('U');
260 pasteMenu.setMnemonic('P');
261 reload.setMnemonic('R');
265 private void jbInit() throws Exception
270 JMenuItem saveAs = new JMenuItem(
271 MessageManager.getString("action.save_as"));
272 ActionListener al = new ActionListener()
275 public void actionPerformed(ActionEvent e)
277 saveAs_actionPerformed();
281 // FIXME getDefaultToolkit throws an exception in Headless mode
282 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
283 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
284 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
286 addMenuActionAndAccelerator(keyStroke, saveAs, al);
288 closeMenuItem.setText(MessageManager.getString("action.close"));
289 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
290 jalview.util.ShortcutKeyMaskExWrapper
291 .getMenuShortcutKeyMaskEx(),
293 al = new ActionListener()
296 public void actionPerformed(ActionEvent e)
298 closeMenuItem_actionPerformed(false);
301 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
303 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
304 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
305 JMenu annotationsMenu = new JMenu(
306 MessageManager.getString("action.annotations"));
307 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
308 colourMenu.setText(MessageManager.getString("action.colour"));
309 JMenu calculateMenu = new JMenu(
310 MessageManager.getString("action.calculate"));
311 webService.setText(MessageManager.getString("action.web_service"));
312 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
313 MessageManager.getString("action.select_all"));
314 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
315 jalview.util.ShortcutKeyMaskExWrapper
316 .getMenuShortcutKeyMaskEx(),
318 al = new ActionListener()
321 public void actionPerformed(ActionEvent e)
323 selectAllSequenceMenuItem_actionPerformed(e);
326 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
328 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
329 MessageManager.getString("action.deselect_all"));
330 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
331 al = new ActionListener()
334 public void actionPerformed(ActionEvent e)
336 deselectAllSequenceMenuItem_actionPerformed(e);
339 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
341 JMenuItem invertSequenceMenuItem = new JMenuItem(
342 MessageManager.getString("action.invert_sequence_selection"));
343 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
344 jalview.util.ShortcutKeyMaskExWrapper
345 .getMenuShortcutKeyMaskEx(),
347 al = new ActionListener()
350 public void actionPerformed(ActionEvent e)
352 invertSequenceMenuItem_actionPerformed(e);
355 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
357 JMenuItem grpsFromSelection = new JMenuItem(
358 MessageManager.getString("action.make_groups_selection"));
359 grpsFromSelection.addActionListener(new ActionListener()
362 public void actionPerformed(ActionEvent e)
364 makeGrpsFromSelection_actionPerformed(e);
367 JMenuItem expandAlignment = new JMenuItem(
368 MessageManager.getString("action.view_flanking_regions"));
369 expandAlignment.setToolTipText(
370 MessageManager.getString("label.view_flanking_regions"));
371 expandAlignment.addActionListener(new ActionListener()
374 public void actionPerformed(ActionEvent e)
379 JMenuItem remove2LeftMenuItem = new JMenuItem(
380 MessageManager.getString("action.remove_left"));
381 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
382 jalview.util.ShortcutKeyMaskExWrapper
383 .getMenuShortcutKeyMaskEx(),
385 al = new ActionListener()
388 public void actionPerformed(ActionEvent e)
390 remove2LeftMenuItem_actionPerformed(e);
393 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
395 JMenuItem remove2RightMenuItem = new JMenuItem(
396 MessageManager.getString("action.remove_right"));
397 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
398 jalview.util.ShortcutKeyMaskExWrapper
399 .getMenuShortcutKeyMaskEx(),
401 al = new ActionListener()
404 public void actionPerformed(ActionEvent e)
406 remove2RightMenuItem_actionPerformed(e);
409 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
411 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
412 MessageManager.getString("action.remove_empty_columns"));
413 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
414 jalview.util.ShortcutKeyMaskExWrapper
415 .getMenuShortcutKeyMaskEx(),
417 al = new ActionListener()
420 public void actionPerformed(ActionEvent e)
422 removeGappedColumnMenuItem_actionPerformed(e);
425 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
427 JMenuItem removeAllGapsMenuItem = new JMenuItem(
428 MessageManager.getString("action.remove_all_gaps"));
429 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
430 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
431 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
433 al = new ActionListener()
436 public void actionPerformed(ActionEvent e)
438 removeAllGapsMenuItem_actionPerformed(e);
441 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
443 JMenuItem justifyLeftMenuItem = new JMenuItem(
444 MessageManager.getString("action.left_justify"));
445 justifyLeftMenuItem.setToolTipText(
446 MessageManager.getString("tooltip.left_justify"));
447 justifyLeftMenuItem.addActionListener(new ActionListener()
450 public void actionPerformed(ActionEvent e)
452 justifyLeftMenuItem_actionPerformed(e);
455 JMenuItem justifyRightMenuItem = new JMenuItem(
456 MessageManager.getString("action.right_justify"));
457 justifyRightMenuItem.setToolTipText(
458 MessageManager.getString("action.left_justify"));
460 justifyRightMenuItem.addActionListener(new ActionListener()
463 public void actionPerformed(ActionEvent e)
465 justifyRightMenuItem_actionPerformed(e);
468 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
469 viewBoxesMenuItem.setState(true);
470 viewBoxesMenuItem.addActionListener(new ActionListener()
473 public void actionPerformed(ActionEvent e)
475 viewBoxesMenuItem_actionPerformed(e);
478 viewTextMenuItem.setText(MessageManager.getString("action.text"));
479 viewTextMenuItem.setState(true);
480 viewTextMenuItem.addActionListener(new ActionListener()
483 public void actionPerformed(ActionEvent e)
485 viewTextMenuItem_actionPerformed(e);
488 showNonconservedMenuItem
489 .setText(MessageManager.getString("label.show_non_conserved"));
490 showNonconservedMenuItem.setState(false);
491 showNonconservedMenuItem.addActionListener(new ActionListener()
494 public void actionPerformed(ActionEvent e)
496 showUnconservedMenuItem_actionPerformed(e);
499 JMenuItem sortPairwiseMenuItem = new JMenuItem(
500 MessageManager.getString("action.by_pairwise_id"));
501 sortPairwiseMenuItem.addActionListener(new ActionListener()
504 public void actionPerformed(ActionEvent e)
506 sortPairwiseMenuItem_actionPerformed(e);
509 JMenuItem sortIDMenuItem = new JMenuItem(
510 MessageManager.getString("action.by_id"));
511 sortIDMenuItem.addActionListener(new ActionListener()
514 public void actionPerformed(ActionEvent e)
516 sortIDMenuItem_actionPerformed(e);
519 JMenuItem sortLengthMenuItem = new JMenuItem(
520 MessageManager.getString("action.by_length"));
521 sortLengthMenuItem.addActionListener(new ActionListener()
524 public void actionPerformed(ActionEvent e)
526 sortLengthMenuItem_actionPerformed(e);
529 JMenuItem sortGroupMenuItem = new JMenuItem(
530 MessageManager.getString("action.by_group"));
531 sortGroupMenuItem.addActionListener(new ActionListener()
534 public void actionPerformed(ActionEvent e)
536 sortGroupMenuItem_actionPerformed(e);
540 JMenuItem removeRedundancyMenuItem = new JMenuItem(
541 MessageManager.getString("action.remove_redundancy"));
542 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
543 jalview.util.ShortcutKeyMaskExWrapper
544 .getMenuShortcutKeyMaskEx(),
546 al = new ActionListener()
549 public void actionPerformed(ActionEvent e)
551 removeRedundancyMenuItem_actionPerformed(e);
554 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
556 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
557 MessageManager.getString("action.pairwise_alignment"));
558 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
561 public void actionPerformed(ActionEvent e)
563 pairwiseAlignmentMenuItem_actionPerformed(e);
567 this.getContentPane().setLayout(new BorderLayout());
568 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
569 statusBar.setBackground(Color.white);
570 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
571 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
572 statusBar.setText(MessageManager.getString("label.status_bar"));
574 .setText(MessageManager.getString("label.out_to_textbox"));
576 annotationPanelMenuItem.setActionCommand("");
577 annotationPanelMenuItem
578 .setText(MessageManager.getString("label.show_annotations"));
579 annotationPanelMenuItem
580 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
581 annotationPanelMenuItem.addActionListener(new ActionListener()
584 public void actionPerformed(ActionEvent e)
586 annotationPanelMenuItem_actionPerformed(e);
589 showAllAlAnnotations.setText(
590 MessageManager.getString("label.show_all_al_annotations"));
591 final boolean isAnnotationPanelShown = annotationPanelMenuItem
593 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
594 showAllAlAnnotations.addActionListener(new ActionListener()
597 public void actionPerformed(ActionEvent e)
599 showAllAnnotations_actionPerformed(false, true);
602 hideAllAlAnnotations.setText(
603 MessageManager.getString("label.hide_all_al_annotations"));
604 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
605 hideAllAlAnnotations.addActionListener(new ActionListener()
608 public void actionPerformed(ActionEvent e)
610 hideAllAnnotations_actionPerformed(false, true);
613 showAllSeqAnnotations.setText(
614 MessageManager.getString("label.show_all_seq_annotations"));
615 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
616 showAllSeqAnnotations.addActionListener(new ActionListener()
619 public void actionPerformed(ActionEvent e)
621 showAllAnnotations_actionPerformed(true, false);
624 hideAllSeqAnnotations.setText(
625 MessageManager.getString("label.hide_all_seq_annotations"));
626 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
627 hideAllSeqAnnotations.addActionListener(new ActionListener()
630 public void actionPerformed(ActionEvent e)
632 hideAllAnnotations_actionPerformed(true, false);
635 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
636 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
637 SequenceAnnotationOrder.NONE.name()));
638 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
639 MessageManager.getString("label.sort_annotations_by_sequence"));
640 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
641 MessageManager.getString("label.sort_annotations_by_label"));
643 sortAnnBySequence.setSelected(
644 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
645 sortAnnBySequence.addActionListener(new ActionListener()
648 public void actionPerformed(ActionEvent e)
650 boolean newState = sortAnnBySequence.getState();
651 sortAnnByLabel.setSelected(false);
652 setAnnotationSortOrder(
653 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
654 : SequenceAnnotationOrder.NONE);
655 sortAnnotations_actionPerformed();
658 sortAnnByLabel.setSelected(
659 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
660 sortAnnByLabel.addActionListener(new ActionListener()
663 public void actionPerformed(ActionEvent e)
665 boolean newState = sortAnnByLabel.getState();
666 sortAnnBySequence.setSelected(false);
667 setAnnotationSortOrder(
668 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
669 : SequenceAnnotationOrder.NONE);
670 sortAnnotations_actionPerformed();
673 colourTextMenuItem = new JCheckBoxMenuItem(
674 MessageManager.getString("label.colour_text"));
675 colourTextMenuItem.addActionListener(new ActionListener()
678 public void actionPerformed(ActionEvent e)
680 colourTextMenuItem_actionPerformed(e);
684 JMenuItem htmlMenuItem = new JMenuItem(
685 MessageManager.getString("label.html"));
686 htmlMenuItem.addActionListener(new ActionListener()
689 public void actionPerformed(ActionEvent e)
691 htmlMenuItem_actionPerformed(e);
695 JMenuItem createBioJS = new JMenuItem(
696 MessageManager.getString("label.biojs_html_export"));
697 createBioJS.addActionListener(new java.awt.event.ActionListener()
700 public void actionPerformed(ActionEvent e)
702 bioJSMenuItem_actionPerformed(e);
706 JMenuItem overviewMenuItem = new JMenuItem(
707 MessageManager.getString("label.overview_window"));
708 overviewMenuItem.addActionListener(new ActionListener()
711 public void actionPerformed(ActionEvent e)
713 overviewMenuItem_actionPerformed(e);
717 undoMenuItem.setEnabled(false);
718 undoMenuItem.setText(MessageManager.getString("action.undo"));
719 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
720 jalview.util.ShortcutKeyMaskExWrapper
721 .getMenuShortcutKeyMaskEx(),
723 al = new ActionListener()
726 public void actionPerformed(ActionEvent e)
728 undoMenuItem_actionPerformed(e);
731 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
733 redoMenuItem.setEnabled(false);
734 redoMenuItem.setText(MessageManager.getString("action.redo"));
735 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
736 jalview.util.ShortcutKeyMaskExWrapper
737 .getMenuShortcutKeyMaskEx(),
739 al = new ActionListener()
742 public void actionPerformed(ActionEvent e)
744 redoMenuItem_actionPerformed(e);
747 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
749 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
750 wrapMenuItem.addActionListener(new ActionListener()
753 public void actionPerformed(ActionEvent e)
755 wrapMenuItem_actionPerformed(e);
759 JMenuItem printMenuItem = new JMenuItem(
760 MessageManager.getString("action.print"));
761 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
762 jalview.util.ShortcutKeyMaskExWrapper
763 .getMenuShortcutKeyMaskEx(),
765 al = new ActionListener()
768 public void actionPerformed(ActionEvent e)
770 printMenuItem_actionPerformed(e);
773 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
776 .setText(MessageManager.getString("action.show_gaps"));
777 renderGapsMenuItem.setState(true);
778 renderGapsMenuItem.addActionListener(new ActionListener()
781 public void actionPerformed(ActionEvent e)
783 renderGapsMenuItem_actionPerformed(e);
787 JMenuItem findMenuItem = new JMenuItem(
788 MessageManager.getString("action.find"));
789 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
790 jalview.util.ShortcutKeyMaskExWrapper
791 .getMenuShortcutKeyMaskEx(),
793 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
794 MessageManager.getString("label.find_tip")));
795 al = new ActionListener()
798 public void actionPerformed(ActionEvent e)
800 findMenuItem_actionPerformed(e);
803 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
805 showSeqFeatures.setText(
806 MessageManager.getString("label.show_sequence_features"));
807 showSeqFeatures.addActionListener(new ActionListener()
810 public void actionPerformed(ActionEvent actionEvent)
812 showSeqFeatures_actionPerformed(actionEvent);
816 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
817 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
818 * void actionPerformed(ActionEvent actionEvent) {
819 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
822 .setText(MessageManager.getString("label.show_database_refs"));
823 showDbRefsMenuitem.addActionListener(new ActionListener()
827 public void actionPerformed(ActionEvent e)
829 showDbRefs_actionPerformed(e);
833 showNpFeatsMenuitem.setText(
834 MessageManager.getString("label.show_non_positional_features"));
835 showNpFeatsMenuitem.addActionListener(new ActionListener()
839 public void actionPerformed(ActionEvent e)
841 showNpFeats_actionPerformed(e);
845 showGroupConservation
846 .setText(MessageManager.getString("label.group_conservation"));
847 showGroupConservation.addActionListener(new ActionListener()
851 public void actionPerformed(ActionEvent e)
853 showGroupConservation_actionPerformed(e);
859 .setText(MessageManager.getString("label.group_consensus"));
860 showGroupConsensus.addActionListener(new ActionListener()
864 public void actionPerformed(ActionEvent e)
866 showGroupConsensus_actionPerformed(e);
870 showConsensusHistogram.setText(
871 MessageManager.getString("label.show_consensus_histogram"));
872 showConsensusHistogram.addActionListener(new ActionListener()
876 public void actionPerformed(ActionEvent e)
878 showConsensusHistogram_actionPerformed(e);
883 .setText(MessageManager.getString("label.show_consensus_logo"));
884 showSequenceLogo.addActionListener(new ActionListener()
888 public void actionPerformed(ActionEvent e)
890 showSequenceLogo_actionPerformed(e);
894 normaliseSequenceLogo
895 .setText(MessageManager.getString("label.norm_consensus_logo"));
896 normaliseSequenceLogo.addActionListener(new ActionListener()
900 public void actionPerformed(ActionEvent e)
902 normaliseSequenceLogo_actionPerformed(e);
906 applyAutoAnnotationSettings
907 .setText(MessageManager.getString("label.apply_all_groups"));
908 applyAutoAnnotationSettings.setState(false);
909 applyAutoAnnotationSettings.setVisible(true);
910 applyAutoAnnotationSettings.addActionListener(new ActionListener()
913 public void actionPerformed(ActionEvent e)
915 applyAutoAnnotationSettings_actionPerformed(e);
919 ButtonGroup buttonGroup = new ButtonGroup();
920 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
921 MessageManager.getString("label.show_first"));
922 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
923 MessageManager.getString("label.show_last"));
924 buttonGroup.add(showAutoFirst);
925 buttonGroup.add(showAutoLast);
926 final boolean autoFirst = Cache
927 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
928 showAutoFirst.setSelected(autoFirst);
929 setShowAutoCalculatedAbove(autoFirst);
930 showAutoFirst.addActionListener(new ActionListener()
933 public void actionPerformed(ActionEvent e)
935 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
936 sortAnnotations_actionPerformed();
939 showAutoLast.setSelected(!showAutoFirst.isSelected());
940 showAutoLast.addActionListener(new ActionListener()
943 public void actionPerformed(ActionEvent e)
945 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
946 sortAnnotations_actionPerformed();
950 JMenuItem deleteGroups = new JMenuItem(
951 MessageManager.getString("action.undefine_groups"));
952 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
953 jalview.util.ShortcutKeyMaskExWrapper
954 .getMenuShortcutKeyMaskEx(),
956 al = new ActionListener()
959 public void actionPerformed(ActionEvent e)
961 deleteGroups_actionPerformed(e);
964 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
966 JMenuItem annotationColumn = new JMenuItem(
967 MessageManager.getString("action.select_by_annotation"));
968 annotationColumn.addActionListener(new ActionListener()
971 public void actionPerformed(ActionEvent e)
973 annotationColumn_actionPerformed(e);
977 JMenuItem createGroup = new JMenuItem(
978 MessageManager.getString("action.create_group"));
979 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
980 jalview.util.ShortcutKeyMaskExWrapper
981 .getMenuShortcutKeyMaskEx(),
983 al = new ActionListener()
986 public void actionPerformed(ActionEvent e)
988 createGroup_actionPerformed(e);
991 addMenuActionAndAccelerator(keyStroke, createGroup, al);
993 JMenuItem unGroup = new JMenuItem(
994 MessageManager.getString("action.remove_group"));
995 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
996 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
997 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
999 al = new ActionListener()
1002 public void actionPerformed(ActionEvent e)
1004 unGroup_actionPerformed(e);
1007 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1009 copy.setText(MessageManager.getString("action.copy"));
1010 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1011 jalview.util.ShortcutKeyMaskExWrapper
1012 .getMenuShortcutKeyMaskEx(),
1015 al = new ActionListener()
1018 public void actionPerformed(ActionEvent e)
1020 copy_actionPerformed();
1023 addMenuActionAndAccelerator(keyStroke, copy, al);
1025 cut.setText(MessageManager.getString("action.cut"));
1026 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1027 jalview.util.ShortcutKeyMaskExWrapper
1028 .getMenuShortcutKeyMaskEx(),
1030 al = new ActionListener()
1033 public void actionPerformed(ActionEvent e)
1035 cut_actionPerformed();
1038 addMenuActionAndAccelerator(keyStroke, cut, al);
1040 JMenuItem delete = new JMenuItem(
1041 MessageManager.getString("action.delete"));
1042 delete.addActionListener(new ActionListener()
1045 public void actionPerformed(ActionEvent e)
1047 delete_actionPerformed();
1051 pasteMenu.setText(MessageManager.getString("action.paste"));
1052 JMenuItem pasteNew = new JMenuItem(
1053 MessageManager.getString("label.to_new_alignment"));
1054 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1055 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1056 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1058 al = new ActionListener()
1061 public void actionPerformed(ActionEvent e)
1063 pasteNew_actionPerformed(e);
1066 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1068 JMenuItem pasteThis = new JMenuItem(
1069 MessageManager.getString("label.to_this_alignment"));
1070 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1071 jalview.util.ShortcutKeyMaskExWrapper
1072 .getMenuShortcutKeyMaskEx(),
1074 al = new ActionListener()
1077 public void actionPerformed(ActionEvent e)
1079 pasteThis_actionPerformed(e);
1082 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1084 JMenuItem createPNG = new JMenuItem("PNG");
1085 createPNG.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 createPNG_actionPerformed(e);
1093 createPNG.setActionCommand(
1094 MessageManager.getString("label.save_png_image"));
1096 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1097 font.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 font_actionPerformed(e);
1106 MessageManager.getString("label.show_sequence_limits"));
1107 seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
1108 seqLimits.addActionListener(new ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 seqLimit_actionPerformed(e);
1116 JMenuItem epsFile = new JMenuItem("EPS");
1117 epsFile.addActionListener(new ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 createEPS_actionPerformed(e);
1126 JMenuItem createSVG = new JMenuItem("SVG");
1127 createSVG.addActionListener(new ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 createSVG_actionPerformed(e);
1136 JMenuItem loadTreeMenuItem = new JMenuItem(
1137 MessageManager.getString("label.load_associated_tree"));
1138 loadTreeMenuItem.setActionCommand(
1139 MessageManager.getString("label.load_tree_for_sequence_set"));
1140 loadTreeMenuItem.addActionListener(new ActionListener()
1143 public void actionPerformed(ActionEvent e)
1145 loadTreeMenuItem_actionPerformed(e);
1149 scaleAbove.setVisible(false);
1150 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1151 scaleAbove.addActionListener(new ActionListener()
1154 public void actionPerformed(ActionEvent e)
1156 scaleAbove_actionPerformed(e);
1159 scaleLeft.setVisible(false);
1160 scaleLeft.setSelected(true);
1161 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1162 scaleLeft.addActionListener(new ActionListener()
1165 public void actionPerformed(ActionEvent e)
1167 scaleLeft_actionPerformed(e);
1170 scaleRight.setVisible(false);
1171 scaleRight.setSelected(true);
1172 scaleRight.setText(MessageManager.getString("action.scale_right"));
1173 scaleRight.addActionListener(new ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 scaleRight_actionPerformed(e);
1181 centreColumnLabelsMenuItem.setVisible(true);
1182 centreColumnLabelsMenuItem.setState(false);
1183 centreColumnLabelsMenuItem.setText(
1184 MessageManager.getString("label.centre_column_labels"));
1185 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 centreColumnLabels_actionPerformed(e);
1193 followHighlightMenuItem.setVisible(true);
1194 followHighlightMenuItem.setState(true);
1195 followHighlightMenuItem
1196 .setText(MessageManager.getString("label.automatic_scrolling"));
1197 followHighlightMenuItem.addActionListener(new ActionListener()
1201 public void actionPerformed(ActionEvent e)
1203 followHighlight_actionPerformed();
1209 .setText(MessageManager.getString("action.by_tree_order"));
1210 sort.setText(MessageManager.getString("action.sort"));
1211 sort.addMenuListener(new MenuListener()
1214 public void menuSelected(MenuEvent e)
1216 buildTreeSortMenu();
1220 public void menuDeselected(MenuEvent e)
1225 public void menuCanceled(MenuEvent e)
1230 .setText(MessageManager.getString("label.sort_by_score"));
1231 sort.add(sortByAnnotScore);
1232 sort.addMenuListener(new javax.swing.event.MenuListener()
1236 public void menuCanceled(MenuEvent e)
1241 public void menuDeselected(MenuEvent e)
1246 public void menuSelected(MenuEvent e)
1248 buildSortByAnnotationScoresMenu();
1251 sortByAnnotScore.setVisible(false);
1254 .setText(MessageManager.getString("action.calculate_tree_pca"));
1256 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1257 padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
1258 padGapsMenuitem.addActionListener(new ActionListener()
1261 public void actionPerformed(ActionEvent e)
1263 padGapsMenuitem_actionPerformed(e);
1266 JMenuItem vamsasStore = new JMenuItem(
1267 MessageManager.getString("label.vamsas_store"));
1268 vamsasStore.setVisible(false);
1269 vamsasStore.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 vamsasStore_actionPerformed(e);
1279 * Translate as cDNA with sub-menu of translation tables
1282 .setText(MessageManager.getString("label.translate_cDNA"));
1283 boolean first = true;
1284 for (final GeneticCodeI table : GeneticCodes.getInstance()
1287 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1288 showTranslation.add(item);
1289 item.addActionListener(new ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 showTranslation_actionPerformed(table);
1299 showTranslation.addSeparator();
1304 showReverse.setText(MessageManager.getString("label.reverse"));
1305 showReverse.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 showReverse_actionPerformed(false);
1313 showReverseComplement
1314 .setText(MessageManager.getString("label.reverse_complement"));
1315 showReverseComplement.addActionListener(new ActionListener()
1318 public void actionPerformed(ActionEvent e)
1320 showReverse_actionPerformed(true);
1324 JMenuItem extractScores = new JMenuItem(
1325 MessageManager.getString("label.extract_scores"));
1326 extractScores.addActionListener(new ActionListener()
1329 public void actionPerformed(ActionEvent e)
1331 extractScores_actionPerformed(e);
1334 extractScores.setVisible(true);
1335 // JBPNote: TODO: make gui for regex based score extraction
1337 // for show products actions see AlignFrame.canShowProducts
1338 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1340 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1341 runGroovy.setToolTipText(
1342 MessageManager.getString("label.run_groovy_tip"));
1343 runGroovy.addActionListener(new ActionListener()
1346 public void actionPerformed(ActionEvent e)
1348 runGroovy_actionPerformed();
1352 openFeatureSettings = new JMenuItem(
1353 MessageManager.getString("action.feature_settings"));
1354 openFeatureSettings.addActionListener(new ActionListener()
1357 public void actionPerformed(ActionEvent e)
1359 featureSettings_actionPerformed(e);
1364 * add sub-menu of database we can fetch from
1366 JMenuItem fetchSequence = new JMenuItem(
1367 MessageManager.getString("label.fetch_sequences"));
1368 fetchSequence.addActionListener(new ActionListener()
1371 public void actionPerformed(ActionEvent e)
1373 fetchSequence_actionPerformed();
1377 JMenuItem associatedData = new JMenuItem(
1378 MessageManager.getString("label.load_features_annotations"));
1379 associatedData.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 associatedData_actionPerformed(e);
1387 loadVcf = new JMenuItem(
1388 MessageManager.getString("label.load_vcf_file"));
1389 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1390 loadVcf.addActionListener(new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 loadVcf_actionPerformed();
1398 autoCalculate.setText(
1399 MessageManager.getString("label.autocalculate_consensus"));
1400 autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1401 autoCalculate.addActionListener(new ActionListener()
1404 public void actionPerformed(ActionEvent e)
1406 autoCalculate_actionPerformed(e);
1410 MessageManager.getString("label.sort_alignment_new_tree"));
1411 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1412 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1413 sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
1414 sortByTree.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent e)
1419 sortByTreeOption_actionPerformed(e);
1423 listenToViewSelections.setText(
1424 MessageManager.getString("label.listen_for_selections"));
1425 listenToViewSelections
1426 .setToolTipText("<html>" + MessageManager.getString(
1427 "label.selections_mirror_selections_made_same_sequences_other_views"));
1428 listenToViewSelections.setState(false);
1429 listenToViewSelections.addActionListener(new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 listenToViewSelections_actionPerformed(e);
1438 JMenu addSequenceMenu = new JMenu(
1439 MessageManager.getString("label.add_sequences"));
1440 JMenuItem addFromFile = new JMenuItem(
1441 MessageManager.getString("label.from_file"));
1442 addFromFile.addActionListener(new ActionListener()
1445 public void actionPerformed(ActionEvent e)
1447 addFromFile_actionPerformed(e);
1450 JMenuItem addFromText = new JMenuItem(
1451 MessageManager.getString("label.from_textbox"));
1452 addFromText.addActionListener(new ActionListener()
1455 public void actionPerformed(ActionEvent e)
1457 addFromText_actionPerformed(e);
1460 JMenuItem addFromURL = new JMenuItem(
1461 MessageManager.getString("label.from_url"));
1462 addFromURL.addActionListener(new ActionListener()
1465 public void actionPerformed(ActionEvent e)
1467 addFromURL_actionPerformed(e);
1470 JMenuItem exportFeatures = new JMenuItem(
1471 MessageManager.getString("label.export_features"));
1472 exportFeatures.addActionListener(new ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 exportFeatures_actionPerformed(e);
1480 JMenuItem exportAnnotations = new JMenuItem(
1481 MessageManager.getString("label.export_annotations"));
1482 exportAnnotations.addActionListener(new ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 exportAnnotations_actionPerformed(e);
1490 statusPanel.setLayout(new GridLayout());
1491 JMenuItem showAllSeqs = new JMenuItem(
1492 MessageManager.getString("label.all_sequences"));
1493 showAllSeqs.setToolTipText(
1494 MessageManager.getString("label.toggle_sequence_visibility"));
1495 showAllSeqs.addActionListener(new ActionListener()
1498 public void actionPerformed(ActionEvent e)
1500 showAllSeqs_actionPerformed(e);
1503 JMenuItem showAllColumns = new JMenuItem(
1504 MessageManager.getString("label.all_columns"));
1505 showAllColumns.setToolTipText(
1506 MessageManager.getString("label.toggle_columns_visibility"));
1507 showAllColumns.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 showAllColumns_actionPerformed(e);
1515 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1516 JMenuItem hideSelSequences = new JMenuItem(
1517 MessageManager.getString("label.selected_sequences"));
1518 hideSelSequences.setToolTipText(
1519 MessageManager.getString("label.toggle_sequence_visibility"));
1520 hideSelSequences.addActionListener(new ActionListener()
1523 public void actionPerformed(ActionEvent e)
1525 hideSelSequences_actionPerformed(e);
1528 JMenuItem hideSelColumns = new JMenuItem(
1529 MessageManager.getString("label.selected_columns"));
1530 hideSelColumns.setToolTipText(
1531 MessageManager.getString("label.toggle_columns_visibility"));
1532 hideSelColumns.addActionListener(new ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 hideSelColumns_actionPerformed(e);
1540 JMenuItem hideAllSelection = new JMenuItem(
1541 MessageManager.getString("label.selected_region"));
1542 hideAllSelection.addActionListener(new ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 hideAllSelection_actionPerformed(e);
1550 // TODO: should be hidden if no selection exists.
1551 JMenuItem hideAllButSelection = new JMenuItem(
1552 MessageManager.getString("label.all_but_selected_region"));
1553 hideAllButSelection.addActionListener(new ActionListener()
1556 public void actionPerformed(ActionEvent e)
1558 hideAllButSelection_actionPerformed(e);
1561 JMenuItem showAllhidden = new JMenuItem(
1562 MessageManager.getString("label.all_sequences_columns"));
1563 showAllhidden.setToolTipText(MessageManager
1564 .getString("label.toggles_visibility_hidden_selected_regions"));
1565 showAllhidden.addActionListener(new ActionListener()
1568 public void actionPerformed(ActionEvent e)
1570 showAllhidden_actionPerformed(e);
1573 hiddenMarkers.setText(
1574 MessageManager.getString("action.show_hidden_markers"));
1575 hiddenMarkers.addActionListener(new ActionListener()
1578 public void actionPerformed(ActionEvent e)
1580 hiddenMarkers_actionPerformed(e);
1584 JMenuItem invertColSel = new JMenuItem(
1585 MessageManager.getString("action.invert_column_selection"));
1586 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1587 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1588 | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1590 al = new ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 invertColSel_actionPerformed(e);
1598 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1600 showComplementMenuItem.setVisible(false);
1601 showComplementMenuItem.addActionListener(new ActionListener()
1604 public void actionPerformed(ActionEvent e)
1606 showComplement_actionPerformed(showComplementMenuItem.getState());
1610 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1613 public void stateChanged(ChangeEvent evt)
1615 JTabbedPane pane = (JTabbedPane) evt.getSource();
1616 int sel = pane.getSelectedIndex();
1617 tabSelectionChanged(sel);
1620 tabbedPane.addMouseListener(new MouseAdapter()
1623 public void mousePressed(MouseEvent e)
1625 if (e.isPopupTrigger()) // Mac
1627 tabbedPane_mousePressed(e);
1632 public void mouseReleased(MouseEvent e)
1634 if (e.isPopupTrigger()) // Windows
1636 tabbedPane_mousePressed(e);
1640 tabbedPane.addFocusListener(new FocusAdapter()
1643 public void focusGained(FocusEvent e)
1645 tabbedPane_focusGained(e);
1649 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1650 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1651 jalview.util.ShortcutKeyMaskExWrapper
1652 .getMenuShortcutKeyMaskEx(),
1654 al = new ActionListener()
1657 public void actionPerformed(ActionEvent e)
1659 save_actionPerformed(e);
1662 addMenuActionAndAccelerator(keyStroke, save, al);
1664 reload.setEnabled(false);
1665 reload.setText(MessageManager.getString("action.reload"));
1666 reload.addActionListener(new ActionListener()
1669 public void actionPerformed(ActionEvent e)
1671 reload_actionPerformed(e);
1675 JMenuItem newView = new JMenuItem(
1676 MessageManager.getString("action.new_view"));
1677 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1678 jalview.util.ShortcutKeyMaskExWrapper
1679 .getMenuShortcutKeyMaskEx(),
1681 al = new ActionListener()
1684 public void actionPerformed(ActionEvent e)
1686 newView_actionPerformed(e);
1689 addMenuActionAndAccelerator(keyStroke, newView, al);
1691 tabbedPane.setToolTipText("<html><i>"
1692 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1695 formatMenu.setText(MessageManager.getString("action.format"));
1696 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1698 idRightAlign.setText(
1699 MessageManager.getString("label.right_align_sequence_id"));
1700 idRightAlign.addActionListener(new ActionListener()
1703 public void actionPerformed(ActionEvent e)
1705 idRightAlign_actionPerformed(e);
1709 gatherViews.setEnabled(false);
1710 gatherViews.setText(MessageManager.getString("action.gather_views"));
1711 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1712 al = new ActionListener()
1715 public void actionPerformed(ActionEvent e)
1717 gatherViews_actionPerformed(e);
1720 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1722 expandViews.setEnabled(false);
1723 expandViews.setText(MessageManager.getString("action.expand_views"));
1724 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1725 al = new ActionListener()
1728 public void actionPerformed(ActionEvent e)
1730 expandViews_actionPerformed(e);
1733 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1735 JMenuItem pageSetup = new JMenuItem(
1736 MessageManager.getString("action.page_setup"));
1737 pageSetup.addActionListener(new ActionListener()
1740 public void actionPerformed(ActionEvent e)
1742 pageSetup_actionPerformed(e);
1745 JMenuItem alignmentProperties = new JMenuItem(
1746 MessageManager.getString("label.alignment_props"));
1747 alignmentProperties.addActionListener(new ActionListener()
1750 public void actionPerformed(ActionEvent actionEvent)
1752 alignmentProperties();
1755 JMenuItem selectHighlighted = new JMenuItem(
1756 MessageManager.getString("action.select_highlighted_columns"));
1757 selectHighlighted.setToolTipText(
1758 MessageManager.getString("tooltip.select_highlighted_columns"));
1759 al = new ActionListener()
1762 public void actionPerformed(ActionEvent actionEvent)
1764 selectHighlightedColumns_actionPerformed(actionEvent);
1767 selectHighlighted.addActionListener(al);
1769 copyHighlighted = new JMenuItem(
1770 MessageManager.getString("action.copy_highlighted_regions"));
1771 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1772 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1773 + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1775 copyHighlighted.setToolTipText(
1776 MessageManager.getString("tooltip.copy_highlighted_regions"));
1777 al = new ActionListener()
1780 public void actionPerformed(ActionEvent actionEvent)
1782 copyHighlightedColumns_actionPerformed(actionEvent);
1785 addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
1786 copyHighlighted.addActionListener(al);
1788 JMenu tooltipSettingsMenu = new JMenu(
1789 MessageManager.getString("label.sequence_id_tooltip"));
1790 JMenu autoAnnMenu = new JMenu(
1791 MessageManager.getString("label.autocalculated_annotation"));
1793 JMenu exportImageMenu = new JMenu(
1794 MessageManager.getString("label.export_image"));
1795 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1796 alignFrameMenuBar.add(fileMenu);
1797 alignFrameMenuBar.add(editMenu);
1798 alignFrameMenuBar.add(selectMenu);
1799 alignFrameMenuBar.add(viewMenu);
1800 alignFrameMenuBar.add(annotationsMenu);
1801 alignFrameMenuBar.add(formatMenu);
1802 alignFrameMenuBar.add(colourMenu);
1803 alignFrameMenuBar.add(calculateMenu);
1804 if (!Platform.isJS())
1806 alignFrameMenuBar.add(webService);
1809 fileMenu.add(fetchSequence);
1810 fileMenu.add(addSequenceMenu);
1811 fileMenu.add(reload);
1812 fileMenu.addSeparator();
1813 fileMenu.add(vamsasStore);
1815 fileMenu.add(saveAs);
1816 fileMenu.add(outputTextboxMenu);
1817 fileMenu.add(pageSetup);
1818 fileMenu.add(printMenuItem);
1819 fileMenu.addSeparator();
1820 fileMenu.add(exportImageMenu);
1821 fileMenu.add(exportFeatures);
1822 fileMenu.add(exportAnnotations);
1823 fileMenu.add(loadTreeMenuItem);
1824 fileMenu.add(associatedData);
1825 if (!Platform.isJS())
1827 fileMenu.add(loadVcf);
1829 fileMenu.addSeparator();
1830 fileMenu.add(closeMenuItem);
1832 pasteMenu.add(pasteNew);
1833 pasteMenu.add(pasteThis);
1834 editMenu.add(undoMenuItem);
1835 editMenu.add(redoMenuItem);
1838 editMenu.add(copyHighlighted);
1839 editMenu.add(pasteMenu);
1840 editMenu.add(delete);
1841 editMenu.addSeparator();
1842 editMenu.add(remove2LeftMenuItem);
1843 editMenu.add(remove2RightMenuItem);
1844 editMenu.add(removeGappedColumnMenuItem);
1845 editMenu.add(removeAllGapsMenuItem);
1846 editMenu.add(removeRedundancyMenuItem);
1847 editMenu.addSeparator();
1849 editMenu.add(justifyLeftMenuItem);
1850 editMenu.add(justifyRightMenuItem);
1852 editMenu.addSeparator();
1853 editMenu.add(padGapsMenuitem);
1855 showMenu.add(showAllColumns);
1856 showMenu.add(showAllSeqs);
1857 showMenu.add(showAllhidden);
1858 hideMenu.add(hideSelColumns);
1859 hideMenu.add(hideSelSequences);
1860 hideMenu.add(hideAllSelection);
1861 hideMenu.add(hideAllButSelection);
1862 viewMenu.add(newView);
1863 viewMenu.add(expandViews);
1864 viewMenu.add(gatherViews);
1865 viewMenu.addSeparator();
1866 viewMenu.add(showMenu);
1867 viewMenu.add(hideMenu);
1868 viewMenu.add(showComplementMenuItem);
1869 viewMenu.addSeparator();
1870 viewMenu.add(followHighlightMenuItem);
1871 viewMenu.addSeparator();
1872 viewMenu.add(showSeqFeatures);
1873 // viewMenu.add(showSeqFeaturesHeight);
1874 viewMenu.add(openFeatureSettings);
1875 tooltipSettingsMenu.add(showDbRefsMenuitem);
1876 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1877 viewMenu.add(tooltipSettingsMenu);
1878 viewMenu.addSeparator();
1879 viewMenu.add(alignmentProperties);
1880 viewMenu.addSeparator();
1881 viewMenu.add(overviewMenuItem);
1883 annotationsMenu.add(annotationPanelMenuItem);
1884 annotationsMenu.addSeparator();
1885 annotationsMenu.add(showAllAlAnnotations);
1886 annotationsMenu.add(hideAllAlAnnotations);
1887 annotationsMenu.addSeparator();
1888 annotationsMenu.add(showAllSeqAnnotations);
1889 annotationsMenu.add(hideAllSeqAnnotations);
1890 annotationsMenu.add(sortAnnBySequence);
1891 annotationsMenu.add(sortAnnByLabel);
1892 annotationsMenu.addSeparator();
1893 autoAnnMenu.add(showAutoFirst);
1894 autoAnnMenu.add(showAutoLast);
1895 autoAnnMenu.addSeparator();
1896 autoAnnMenu.add(applyAutoAnnotationSettings);
1897 autoAnnMenu.add(showConsensusHistogram);
1898 autoAnnMenu.add(showSequenceLogo);
1899 autoAnnMenu.add(normaliseSequenceLogo);
1900 autoAnnMenu.addSeparator();
1901 autoAnnMenu.add(showGroupConservation);
1902 autoAnnMenu.add(showGroupConsensus);
1903 annotationsMenu.add(autoAnnMenu);
1905 sort.add(sortIDMenuItem);
1906 sort.add(sortLengthMenuItem);
1907 sort.add(sortGroupMenuItem);
1908 sort.add(sortPairwiseMenuItem);
1909 sort.add(sortByTreeMenu);
1910 calculateMenu.add(sort);
1911 calculateMenu.add(calculateTree);
1912 calculateMenu.addSeparator();
1913 calculateMenu.add(pairwiseAlignmentMenuItem);
1914 calculateMenu.addSeparator();
1915 calculateMenu.add(showTranslation);
1916 calculateMenu.add(showReverse);
1917 calculateMenu.add(showReverseComplement);
1918 calculateMenu.add(showProducts);
1919 calculateMenu.add(autoCalculate);
1920 calculateMenu.add(sortByTree);
1921 calculateMenu.addSeparator();
1922 calculateMenu.add(expandAlignment);
1923 calculateMenu.add(extractScores);
1924 if (!Platform.isJS())
1926 calculateMenu.addSeparator();
1927 calculateMenu.add(runGroovy);
1930 webServiceNoServices = new JMenuItem(
1931 MessageManager.getString("label.no_services"));
1932 webService.add(webServiceNoServices);
1933 if (!Platform.isJS())
1935 exportImageMenu.add(htmlMenuItem);
1937 exportImageMenu.add(epsFile);
1938 exportImageMenu.add(createPNG);
1939 if (!Platform.isJS())
1941 exportImageMenu.add(createBioJS);
1942 exportImageMenu.add(createSVG);
1944 addSequenceMenu.add(addFromFile);
1945 addSequenceMenu.add(addFromText);
1946 addSequenceMenu.add(addFromURL);
1947 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1948 statusPanel.add(statusBar, null);
1949 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1951 formatMenu.add(font);
1952 formatMenu.addSeparator();
1953 formatMenu.add(wrapMenuItem);
1954 formatMenu.add(scaleAbove);
1955 formatMenu.add(scaleLeft);
1956 formatMenu.add(scaleRight);
1957 formatMenu.add(seqLimits);
1958 formatMenu.add(idRightAlign);
1959 formatMenu.add(hiddenMarkers);
1960 formatMenu.add(viewBoxesMenuItem);
1961 formatMenu.add(viewTextMenuItem);
1962 formatMenu.add(colourTextMenuItem);
1963 formatMenu.add(renderGapsMenuItem);
1964 formatMenu.add(centreColumnLabelsMenuItem);
1965 formatMenu.add(showNonconservedMenuItem);
1966 selectMenu.add(findMenuItem);
1967 selectMenu.addSeparator();
1968 selectMenu.add(selectAllSequenceMenuItem);
1969 selectMenu.add(deselectAllSequenceMenuItem);
1970 selectMenu.add(invertSequenceMenuItem);
1971 selectMenu.add(invertColSel);
1972 selectMenu.add(createGroup);
1973 selectMenu.add(unGroup);
1974 selectMenu.add(grpsFromSelection);
1975 selectMenu.add(deleteGroups);
1976 selectMenu.add(annotationColumn);
1977 selectMenu.add(selectHighlighted);
1978 // TODO - determine if the listenToViewSelections button is needed : see bug
1980 // selectMenu.addSeparator();
1981 // selectMenu.add(listenToViewSelections);
1984 protected void createPNG_actionPerformed(ActionEvent object)
1986 // TODO Auto-generated method stub
1990 protected void createEPS_actionPerformed(ActionEvent object)
1992 // TODO Auto-generated method stub
1996 protected void createSVG_actionPerformed(ActionEvent object)
1998 // TODO Auto-generated method stub
2002 protected void copyHighlightedColumns_actionPerformed(
2003 ActionEvent actionEvent)
2008 protected void loadVcf_actionPerformed()
2013 * Constructs the entries on the Colour menu (but does not add them to the
2016 protected void initColourMenu()
2018 applyToAllGroups = new JCheckBoxMenuItem(
2019 MessageManager.getString("label.apply_colour_to_all_groups"));
2020 applyToAllGroups.addActionListener(new ActionListener()
2023 public void actionPerformed(ActionEvent e)
2025 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2029 textColour = new JMenuItem(
2030 MessageManager.getString("label.text_colour"));
2031 textColour.addActionListener(new ActionListener()
2034 public void actionPerformed(ActionEvent e)
2036 textColour_actionPerformed();
2040 conservationMenuItem = new JCheckBoxMenuItem(
2041 MessageManager.getString("action.by_conservation"));
2042 conservationMenuItem.addActionListener(new ActionListener()
2045 public void actionPerformed(ActionEvent e)
2047 conservationMenuItem_actionPerformed(
2048 conservationMenuItem.isSelected());
2052 abovePIDThreshold = new JCheckBoxMenuItem(
2053 MessageManager.getString("label.above_identity_threshold"));
2054 abovePIDThreshold.addActionListener(new ActionListener()
2057 public void actionPerformed(ActionEvent e)
2059 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2062 modifyPID = new JMenuItem(
2063 MessageManager.getString("label.modify_identity_threshold"));
2064 modifyPID.addActionListener(new ActionListener()
2067 public void actionPerformed(ActionEvent e)
2069 modifyPID_actionPerformed();
2072 modifyConservation = new JMenuItem(MessageManager
2073 .getString("label.modify_conservation_threshold"));
2074 modifyConservation.addActionListener(new ActionListener()
2077 public void actionPerformed(ActionEvent e)
2079 modifyConservation_actionPerformed();
2083 annotationColour = new JRadioButtonMenuItem(
2084 MessageManager.getString("action.by_annotation"));
2085 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2086 annotationColour.addActionListener(new ActionListener()
2089 public void actionPerformed(ActionEvent e)
2091 annotationColour_actionPerformed();
2096 protected void selectHighlightedColumns_actionPerformed(
2097 ActionEvent actionEvent)
2099 // TODO Auto-generated method stub
2104 * Generate the reverse sequence (or reverse complement if the flag is true)
2105 * and add it to the alignment
2109 protected void showReverse_actionPerformed(boolean complement)
2114 * Try to run script in a Groovy console, having first ensured that this
2115 * alignframe is set as currentAlignFrame in Desktop
2117 protected void runGroovy_actionPerformed()
2123 * Adds the given action listener and key accelerator to the given menu item.
2124 * Also saves in a lookup table to support lookup of action by key stroke.
2128 * @param actionListener
2130 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2131 JMenuItem menuItem, ActionListener actionListener)
2133 menuItem.setAccelerator(keyStroke);
2134 accelerators.put(keyStroke, menuItem);
2135 menuItem.addActionListener(actionListener);
2139 * Action on clicking sort annotations by type.
2143 protected void sortAnnotations_actionPerformed()
2148 * Action on clicking Show all annotations.
2150 * @param forSequences
2151 * update sequence-related annotations
2152 * @param forAlignment
2153 * update non-sequence-related annotations
2155 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2156 boolean forAlignment)
2158 setAnnotationsVisibility(true, forSequences, forAlignment);
2162 * Action on clicking Hide all annotations.
2164 * @param forSequences
2165 * update sequence-related annotations
2166 * @param forAlignment
2167 * update non-sequence-related annotations
2169 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2170 boolean forAlignment)
2172 setAnnotationsVisibility(false, forSequences, forAlignment);
2176 * Set the visibility of annotations to true or false. Can act on
2177 * sequence-related annotations, or alignment-related, or both.
2180 * @param forSequences
2181 * update sequence-related annotations
2182 * @param forAlignment
2183 * update non-sequence-related annotations
2185 public void setAnnotationsVisibility(boolean visible,
2186 boolean forSequences, boolean forAlignment)
2191 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2193 // TODO Auto-generated method stub
2197 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2199 // TODO Auto-generated method stub
2203 protected void showAllhidden_actionPerformed(ActionEvent e)
2205 // TODO Auto-generated method stub
2209 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2211 // TODO Auto-generated method stub
2215 protected void hideAllSelection_actionPerformed(ActionEvent e)
2217 // TODO Auto-generated method stub
2221 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2223 // TODO Auto-generated method stub
2227 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2229 // TODO Auto-generated method stub
2233 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2235 // TODO Auto-generated method stub
2239 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2241 // TODO Auto-generated method stub
2245 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2247 // TODO Auto-generated method stub
2251 protected void showGroupConservation_actionPerformed(ActionEvent e)
2253 // TODO Auto-generated method stub
2257 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2259 // TODO Auto-generated method stub
2263 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2265 // TODO Auto-generated method stub
2269 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2271 // TODO Auto-generated method stub
2275 protected void followHighlight_actionPerformed()
2277 // TODO Auto-generated method stub
2281 protected void showNpFeats_actionPerformed(ActionEvent e)
2283 // TODO Auto-generated method stub
2287 protected void showDbRefs_actionPerformed(ActionEvent e)
2289 // TODO Auto-generated method stub
2293 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2297 protected void buildSortByAnnotationScoresMenu()
2301 protected void extractScores_actionPerformed(ActionEvent e)
2305 protected void outputText_actionPerformed(String formatName)
2309 public void addFromFile_actionPerformed(ActionEvent e)
2314 public void addFromText_actionPerformed(ActionEvent e)
2319 public void addFromURL_actionPerformed(ActionEvent e)
2324 public void exportFeatures_actionPerformed(ActionEvent e)
2329 public void exportAnnotations_actionPerformed(ActionEvent e)
2334 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2338 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2343 protected void closeMenuItem_actionPerformed(boolean b)
2347 protected void redoMenuItem_actionPerformed(ActionEvent e)
2351 protected void undoMenuItem_actionPerformed(ActionEvent e)
2355 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2359 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2363 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2367 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2371 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2375 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2379 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2383 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2387 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2391 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2395 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2399 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2403 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2407 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2411 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2415 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2419 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2423 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2427 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2431 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2435 protected void conservationMenuItem_actionPerformed(boolean selected)
2439 protected void printMenuItem_actionPerformed(ActionEvent e)
2443 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2447 protected void findMenuItem_actionPerformed(ActionEvent e)
2451 protected void abovePIDThreshold_actionPerformed(boolean selected)
2455 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2459 protected void deleteGroups_actionPerformed(ActionEvent e)
2463 protected void createGroup_actionPerformed(ActionEvent e)
2467 protected void unGroup_actionPerformed(ActionEvent e)
2471 protected void copy_actionPerformed()
2475 protected void cut_actionPerformed()
2479 protected void delete_actionPerformed()
2483 protected void pasteNew_actionPerformed(ActionEvent e)
2487 protected void pasteThis_actionPerformed(ActionEvent e)
2491 protected void applyToAllGroups_actionPerformed(boolean selected)
2495 protected void font_actionPerformed(ActionEvent e)
2499 protected void seqLimit_actionPerformed(ActionEvent e)
2503 public void seqDBRef_actionPerformed(ActionEvent e)
2508 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2514 * Template method to handle the 'load T-Coffee scores' menu event.
2516 * Subclasses override this method to provide a custom action.
2521 protected void loadScores_actionPerformed(ActionEvent event)
2526 protected void jpred_actionPerformed(ActionEvent e)
2530 protected void scaleAbove_actionPerformed(ActionEvent e)
2534 protected void scaleLeft_actionPerformed(ActionEvent e)
2538 protected void scaleRight_actionPerformed(ActionEvent e)
2542 protected void modifyPID_actionPerformed()
2546 protected void modifyConservation_actionPerformed()
2550 protected void saveAs_actionPerformed()
2554 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2558 public void vamsasStore_actionPerformed(ActionEvent e)
2563 public void vamsasLoad_actionPerformed(ActionEvent e)
2568 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2573 public void featureSettings_actionPerformed(ActionEvent e)
2578 public void fetchSequence_actionPerformed()
2583 public void smoothFont_actionPerformed(ActionEvent e)
2588 public void annotationColour_actionPerformed()
2592 public void annotationColumn_actionPerformed(ActionEvent e)
2596 public void associatedData_actionPerformed(ActionEvent e)
2601 public void autoCalculate_actionPerformed(ActionEvent e)
2606 public void sortByTreeOption_actionPerformed(ActionEvent e)
2611 public void showAllSeqs_actionPerformed(ActionEvent e)
2616 public void showAllColumns_actionPerformed(ActionEvent e)
2621 public void hideSelSequences_actionPerformed(ActionEvent e)
2626 public void hideSelColumns_actionPerformed(ActionEvent e)
2631 public void hiddenMarkers_actionPerformed(ActionEvent e)
2636 public void findPdbId_actionPerformed(ActionEvent e)
2641 public void enterPdbId_actionPerformed(ActionEvent e)
2646 public void pdbFile_actionPerformed(ActionEvent e)
2651 public void invertColSel_actionPerformed(ActionEvent e)
2656 public void tabSelectionChanged(int sel)
2661 public void tabbedPane_mousePressed(MouseEvent e)
2666 public void tabbedPane_focusGained(FocusEvent e)
2671 public void save_actionPerformed(ActionEvent e)
2676 public void reload_actionPerformed(ActionEvent e)
2681 public void newView_actionPerformed(ActionEvent e)
2686 public void textColour_actionPerformed()
2691 public void idRightAlign_actionPerformed(ActionEvent e)
2696 public void expandViews_actionPerformed(ActionEvent e)
2701 public void gatherViews_actionPerformed(ActionEvent e)
2706 public void buildTreeSortMenu()
2711 public void pageSetup_actionPerformed(ActionEvent e)
2716 public void alignmentProperties()
2721 protected void expand_newalign(ActionEvent e)
2723 // TODO Auto-generated method stub
2727 protected boolean isShowAutoCalculatedAbove()
2729 return showAutoCalculatedAbove;
2732 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2734 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2737 protected SequenceAnnotationOrder getAnnotationSortOrder()
2739 return annotationSortOrder;
2742 protected void setAnnotationSortOrder(
2743 SequenceAnnotationOrder annotationSortOrder)
2745 this.annotationSortOrder = annotationSortOrder;
2748 public Map<KeyStroke, JMenuItem> getAccelerators()
2750 return this.accelerators;
2754 * Returns the selected index of the tabbed pane, or -1 if none selected
2755 * (including the case where the tabbed pane has not been made visible).
2759 public int getTabIndex()
2761 return tabbedPane.getSelectedIndex();
2764 public JPanel getStatusPanel()
2770 * Sets a reference to the containing split frame. Also makes the 'toggle
2771 * split view' menu item visible and checked.
2775 public void setSplitFrame(SplitContainerI sf)
2777 this.splitFrame = sf;
2780 this.showComplementMenuItem.setVisible(true);
2781 this.showComplementMenuItem.setState(true);
2785 public SplitContainerI getSplitViewContainer()
2787 return this.splitFrame;
2790 protected void showComplement_actionPerformed(boolean complement)