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;
224 // for Web-page embedding using id=align-frame-div
225 setName("jalview-alignment");
228 setJMenuBar(alignFrameMenuBar);
230 // dynamically fill save as menu with available formats
231 for (String ff : FileFormats.getInstance().getWritableFormats(true))
233 JMenuItem item = new JMenuItem(ff);
235 item.addActionListener(new ActionListener()
238 public void actionPerformed(ActionEvent e)
240 outputText_actionPerformed(e.getActionCommand());
244 outputTextboxMenu.add(item);
246 } catch (Exception e)
248 System.err.println(e.toString());
251 if (Platform.allowMnemonics()) // was "not mac and not JS"
253 closeMenuItem.setMnemonic('C');
254 outputTextboxMenu.setMnemonic('T');
255 undoMenuItem.setMnemonic('Z');
256 redoMenuItem.setMnemonic('0');
257 copy.setMnemonic('C');
258 cut.setMnemonic('U');
259 pasteMenu.setMnemonic('P');
260 reload.setMnemonic('R');
264 private void jbInit() throws Exception
268 JMenuItem saveAs = new JMenuItem(
269 MessageManager.getString("action.save_as"));
270 ActionListener al = new ActionListener()
273 public void actionPerformed(ActionEvent e)
275 saveAs_actionPerformed();
279 // FIXME getDefaultToolkit throws an exception in Headless mode
280 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
281 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
282 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
284 addMenuActionAndAccelerator(keyStroke, saveAs, al);
286 closeMenuItem.setText(MessageManager.getString("action.close"));
287 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
288 jalview.util.ShortcutKeyMaskExWrapper
289 .getMenuShortcutKeyMaskEx(),
291 al = new ActionListener()
294 public void actionPerformed(ActionEvent e)
296 closeMenuItem_actionPerformed(false);
299 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
301 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
302 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
303 JMenu annotationsMenu = new JMenu(
304 MessageManager.getString("action.annotations"));
305 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
306 colourMenu.setText(MessageManager.getString("action.colour"));
307 JMenu calculateMenu = new JMenu(
308 MessageManager.getString("action.calculate"));
309 webService.setText(MessageManager.getString("action.web_service"));
310 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
311 MessageManager.getString("action.select_all"));
312 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
313 jalview.util.ShortcutKeyMaskExWrapper
314 .getMenuShortcutKeyMaskEx(),
316 al = new ActionListener()
319 public void actionPerformed(ActionEvent e)
321 selectAllSequenceMenuItem_actionPerformed(e);
324 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
326 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
327 MessageManager.getString("action.deselect_all"));
328 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
329 al = new ActionListener()
332 public void actionPerformed(ActionEvent e)
334 deselectAllSequenceMenuItem_actionPerformed(e);
337 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
339 JMenuItem invertSequenceMenuItem = new JMenuItem(
340 MessageManager.getString("action.invert_sequence_selection"));
341 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
342 jalview.util.ShortcutKeyMaskExWrapper
343 .getMenuShortcutKeyMaskEx(),
345 al = new ActionListener()
348 public void actionPerformed(ActionEvent e)
350 invertSequenceMenuItem_actionPerformed(e);
353 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
355 JMenuItem grpsFromSelection = new JMenuItem(
356 MessageManager.getString("action.make_groups_selection"));
357 grpsFromSelection.addActionListener(new ActionListener()
360 public void actionPerformed(ActionEvent e)
362 makeGrpsFromSelection_actionPerformed(e);
365 JMenuItem expandAlignment = new JMenuItem(
366 MessageManager.getString("action.view_flanking_regions"));
367 expandAlignment.setToolTipText(
368 MessageManager.getString("label.view_flanking_regions"));
369 expandAlignment.addActionListener(new ActionListener()
372 public void actionPerformed(ActionEvent e)
377 JMenuItem remove2LeftMenuItem = new JMenuItem(
378 MessageManager.getString("action.remove_left"));
379 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
380 jalview.util.ShortcutKeyMaskExWrapper
381 .getMenuShortcutKeyMaskEx(),
383 al = new ActionListener()
386 public void actionPerformed(ActionEvent e)
388 remove2LeftMenuItem_actionPerformed(e);
391 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
393 JMenuItem remove2RightMenuItem = new JMenuItem(
394 MessageManager.getString("action.remove_right"));
395 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
396 jalview.util.ShortcutKeyMaskExWrapper
397 .getMenuShortcutKeyMaskEx(),
399 al = new ActionListener()
402 public void actionPerformed(ActionEvent e)
404 remove2RightMenuItem_actionPerformed(e);
407 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
409 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
410 MessageManager.getString("action.remove_empty_columns"));
411 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
412 jalview.util.ShortcutKeyMaskExWrapper
413 .getMenuShortcutKeyMaskEx(),
415 al = new ActionListener()
418 public void actionPerformed(ActionEvent e)
420 removeGappedColumnMenuItem_actionPerformed(e);
423 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
425 JMenuItem removeAllGapsMenuItem = new JMenuItem(
426 MessageManager.getString("action.remove_all_gaps"));
427 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
428 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
429 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
431 al = new ActionListener()
434 public void actionPerformed(ActionEvent e)
436 removeAllGapsMenuItem_actionPerformed(e);
439 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
441 JMenuItem justifyLeftMenuItem = new JMenuItem(
442 MessageManager.getString("action.left_justify_alignment"));
443 justifyLeftMenuItem.addActionListener(new ActionListener()
446 public void actionPerformed(ActionEvent e)
448 justifyLeftMenuItem_actionPerformed(e);
451 JMenuItem justifyRightMenuItem = new JMenuItem(
452 MessageManager.getString("action.right_justify_alignment"));
453 justifyRightMenuItem.addActionListener(new ActionListener()
456 public void actionPerformed(ActionEvent e)
458 justifyRightMenuItem_actionPerformed(e);
461 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
462 viewBoxesMenuItem.setState(true);
463 viewBoxesMenuItem.addActionListener(new ActionListener()
466 public void actionPerformed(ActionEvent e)
468 viewBoxesMenuItem_actionPerformed(e);
471 viewTextMenuItem.setText(MessageManager.getString("action.text"));
472 viewTextMenuItem.setState(true);
473 viewTextMenuItem.addActionListener(new ActionListener()
476 public void actionPerformed(ActionEvent e)
478 viewTextMenuItem_actionPerformed(e);
481 showNonconservedMenuItem
482 .setText(MessageManager.getString("label.show_non_conserved"));
483 showNonconservedMenuItem.setState(false);
484 showNonconservedMenuItem.addActionListener(new ActionListener()
487 public void actionPerformed(ActionEvent e)
489 showUnconservedMenuItem_actionPerformed(e);
492 JMenuItem sortPairwiseMenuItem = new JMenuItem(
493 MessageManager.getString("action.by_pairwise_id"));
494 sortPairwiseMenuItem.addActionListener(new ActionListener()
497 public void actionPerformed(ActionEvent e)
499 sortPairwiseMenuItem_actionPerformed(e);
502 JMenuItem sortIDMenuItem = new JMenuItem(
503 MessageManager.getString("action.by_id"));
504 sortIDMenuItem.addActionListener(new ActionListener()
507 public void actionPerformed(ActionEvent e)
509 sortIDMenuItem_actionPerformed(e);
512 JMenuItem sortLengthMenuItem = new JMenuItem(
513 MessageManager.getString("action.by_length"));
514 sortLengthMenuItem.addActionListener(new ActionListener()
517 public void actionPerformed(ActionEvent e)
519 sortLengthMenuItem_actionPerformed(e);
522 JMenuItem sortGroupMenuItem = new JMenuItem(
523 MessageManager.getString("action.by_group"));
524 sortGroupMenuItem.addActionListener(new ActionListener()
527 public void actionPerformed(ActionEvent e)
529 sortGroupMenuItem_actionPerformed(e);
533 JMenuItem removeRedundancyMenuItem = new JMenuItem(
534 MessageManager.getString("action.remove_redundancy"));
535 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
536 jalview.util.ShortcutKeyMaskExWrapper
537 .getMenuShortcutKeyMaskEx(),
539 al = new ActionListener()
542 public void actionPerformed(ActionEvent e)
544 removeRedundancyMenuItem_actionPerformed(e);
547 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
549 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
550 MessageManager.getString("action.pairwise_alignment"));
551 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
554 public void actionPerformed(ActionEvent e)
556 pairwiseAlignmentMenuItem_actionPerformed(e);
560 this.getContentPane().setLayout(new BorderLayout());
561 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
562 statusBar.setBackground(Color.white);
563 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
564 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
565 statusBar.setText(MessageManager.getString("label.status_bar"));
567 .setText(MessageManager.getString("label.out_to_textbox"));
569 annotationPanelMenuItem.setActionCommand("");
570 annotationPanelMenuItem
571 .setText(MessageManager.getString("label.show_annotations"));
572 annotationPanelMenuItem
573 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
574 annotationPanelMenuItem.addActionListener(new ActionListener()
577 public void actionPerformed(ActionEvent e)
579 annotationPanelMenuItem_actionPerformed(e);
582 showAllAlAnnotations.setText(
583 MessageManager.getString("label.show_all_al_annotations"));
584 final boolean isAnnotationPanelShown = annotationPanelMenuItem
586 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
587 showAllAlAnnotations.addActionListener(new ActionListener()
590 public void actionPerformed(ActionEvent e)
592 showAllAnnotations_actionPerformed(false, true);
595 hideAllAlAnnotations.setText(
596 MessageManager.getString("label.hide_all_al_annotations"));
597 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
598 hideAllAlAnnotations.addActionListener(new ActionListener()
601 public void actionPerformed(ActionEvent e)
603 hideAllAnnotations_actionPerformed(false, true);
606 showAllSeqAnnotations.setText(
607 MessageManager.getString("label.show_all_seq_annotations"));
608 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
609 showAllSeqAnnotations.addActionListener(new ActionListener()
612 public void actionPerformed(ActionEvent e)
614 showAllAnnotations_actionPerformed(true, false);
617 hideAllSeqAnnotations.setText(
618 MessageManager.getString("label.hide_all_seq_annotations"));
619 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
620 hideAllSeqAnnotations.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent e)
625 hideAllAnnotations_actionPerformed(true, false);
628 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
629 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
630 SequenceAnnotationOrder.NONE.name()));
631 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
632 MessageManager.getString("label.sort_annotations_by_sequence"));
633 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
634 MessageManager.getString("label.sort_annotations_by_label"));
636 sortAnnBySequence.setSelected(
637 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
638 sortAnnBySequence.addActionListener(new ActionListener()
641 public void actionPerformed(ActionEvent e)
643 boolean newState = sortAnnBySequence.getState();
644 sortAnnByLabel.setSelected(false);
645 setAnnotationSortOrder(
646 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
647 : SequenceAnnotationOrder.NONE);
648 sortAnnotations_actionPerformed();
651 sortAnnByLabel.setSelected(
652 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
653 sortAnnByLabel.addActionListener(new ActionListener()
656 public void actionPerformed(ActionEvent e)
658 boolean newState = sortAnnByLabel.getState();
659 sortAnnBySequence.setSelected(false);
660 setAnnotationSortOrder(
661 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
662 : SequenceAnnotationOrder.NONE);
663 sortAnnotations_actionPerformed();
666 colourTextMenuItem = new JCheckBoxMenuItem(
667 MessageManager.getString("label.colour_text"));
668 colourTextMenuItem.addActionListener(new ActionListener()
671 public void actionPerformed(ActionEvent e)
673 colourTextMenuItem_actionPerformed(e);
677 JMenuItem htmlMenuItem = new JMenuItem(
678 MessageManager.getString("label.html"));
679 htmlMenuItem.addActionListener(new ActionListener()
682 public void actionPerformed(ActionEvent e)
684 htmlMenuItem_actionPerformed(e);
688 JMenuItem createBioJS = new JMenuItem(
689 MessageManager.getString("label.biojs_html_export"));
690 createBioJS.addActionListener(new java.awt.event.ActionListener()
693 public void actionPerformed(ActionEvent e)
695 bioJSMenuItem_actionPerformed(e);
699 JMenuItem overviewMenuItem = new JMenuItem(
700 MessageManager.getString("label.overview_window"));
701 overviewMenuItem.addActionListener(new ActionListener()
704 public void actionPerformed(ActionEvent e)
706 overviewMenuItem_actionPerformed(e);
710 undoMenuItem.setEnabled(false);
711 undoMenuItem.setText(MessageManager.getString("action.undo"));
712 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
713 jalview.util.ShortcutKeyMaskExWrapper
714 .getMenuShortcutKeyMaskEx(),
716 al = new ActionListener()
719 public void actionPerformed(ActionEvent e)
721 undoMenuItem_actionPerformed(e);
724 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
726 redoMenuItem.setEnabled(false);
727 redoMenuItem.setText(MessageManager.getString("action.redo"));
728 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
729 jalview.util.ShortcutKeyMaskExWrapper
730 .getMenuShortcutKeyMaskEx(),
732 al = new ActionListener()
735 public void actionPerformed(ActionEvent e)
737 redoMenuItem_actionPerformed(e);
740 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
742 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
743 wrapMenuItem.addActionListener(new ActionListener()
746 public void actionPerformed(ActionEvent e)
748 wrapMenuItem_actionPerformed(e);
752 JMenuItem printMenuItem = new JMenuItem(
753 MessageManager.getString("action.print"));
754 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
755 jalview.util.ShortcutKeyMaskExWrapper
756 .getMenuShortcutKeyMaskEx(),
758 al = new ActionListener()
761 public void actionPerformed(ActionEvent e)
763 printMenuItem_actionPerformed(e);
766 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
769 .setText(MessageManager.getString("action.show_gaps"));
770 renderGapsMenuItem.setState(true);
771 renderGapsMenuItem.addActionListener(new ActionListener()
774 public void actionPerformed(ActionEvent e)
776 renderGapsMenuItem_actionPerformed(e);
780 JMenuItem findMenuItem = new JMenuItem(
781 MessageManager.getString("action.find"));
782 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
783 jalview.util.ShortcutKeyMaskExWrapper
784 .getMenuShortcutKeyMaskEx(),
786 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
787 MessageManager.getString("label.find_tip")));
788 al = new ActionListener()
791 public void actionPerformed(ActionEvent e)
793 findMenuItem_actionPerformed(e);
796 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
798 showSeqFeatures.setText(
799 MessageManager.getString("label.show_sequence_features"));
800 showSeqFeatures.addActionListener(new ActionListener()
803 public void actionPerformed(ActionEvent actionEvent)
805 showSeqFeatures_actionPerformed(actionEvent);
809 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
810 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
811 * void actionPerformed(ActionEvent actionEvent) {
812 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
815 .setText(MessageManager.getString("label.show_database_refs"));
816 showDbRefsMenuitem.addActionListener(new ActionListener()
820 public void actionPerformed(ActionEvent e)
822 showDbRefs_actionPerformed(e);
826 showNpFeatsMenuitem.setText(
827 MessageManager.getString("label.show_non_positional_features"));
828 showNpFeatsMenuitem.addActionListener(new ActionListener()
832 public void actionPerformed(ActionEvent e)
834 showNpFeats_actionPerformed(e);
838 showGroupConservation
839 .setText(MessageManager.getString("label.group_conservation"));
840 showGroupConservation.addActionListener(new ActionListener()
844 public void actionPerformed(ActionEvent e)
846 showGroupConservation_actionPerformed(e);
852 .setText(MessageManager.getString("label.group_consensus"));
853 showGroupConsensus.addActionListener(new ActionListener()
857 public void actionPerformed(ActionEvent e)
859 showGroupConsensus_actionPerformed(e);
863 showConsensusHistogram.setText(
864 MessageManager.getString("label.show_consensus_histogram"));
865 showConsensusHistogram.addActionListener(new ActionListener()
869 public void actionPerformed(ActionEvent e)
871 showConsensusHistogram_actionPerformed(e);
876 .setText(MessageManager.getString("label.show_consensus_logo"));
877 showSequenceLogo.addActionListener(new ActionListener()
881 public void actionPerformed(ActionEvent e)
883 showSequenceLogo_actionPerformed(e);
887 normaliseSequenceLogo
888 .setText(MessageManager.getString("label.norm_consensus_logo"));
889 normaliseSequenceLogo.addActionListener(new ActionListener()
893 public void actionPerformed(ActionEvent e)
895 normaliseSequenceLogo_actionPerformed(e);
899 applyAutoAnnotationSettings
900 .setText(MessageManager.getString("label.apply_all_groups"));
901 applyAutoAnnotationSettings.setState(false);
902 applyAutoAnnotationSettings.setVisible(true);
903 applyAutoAnnotationSettings.addActionListener(new ActionListener()
906 public void actionPerformed(ActionEvent e)
908 applyAutoAnnotationSettings_actionPerformed(e);
912 ButtonGroup buttonGroup = new ButtonGroup();
913 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
914 MessageManager.getString("label.show_first"));
915 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
916 MessageManager.getString("label.show_last"));
917 buttonGroup.add(showAutoFirst);
918 buttonGroup.add(showAutoLast);
919 final boolean autoFirst = Cache
920 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
921 showAutoFirst.setSelected(autoFirst);
922 setShowAutoCalculatedAbove(autoFirst);
923 showAutoFirst.addActionListener(new ActionListener()
926 public void actionPerformed(ActionEvent e)
928 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
929 sortAnnotations_actionPerformed();
932 showAutoLast.setSelected(!showAutoFirst.isSelected());
933 showAutoLast.addActionListener(new ActionListener()
936 public void actionPerformed(ActionEvent e)
938 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
939 sortAnnotations_actionPerformed();
943 JMenuItem deleteGroups = new JMenuItem(
944 MessageManager.getString("action.undefine_groups"));
945 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
946 jalview.util.ShortcutKeyMaskExWrapper
947 .getMenuShortcutKeyMaskEx(),
949 al = new ActionListener()
952 public void actionPerformed(ActionEvent e)
954 deleteGroups_actionPerformed(e);
957 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
959 JMenuItem annotationColumn = new JMenuItem(
960 MessageManager.getString("action.select_by_annotation"));
961 annotationColumn.addActionListener(new ActionListener()
964 public void actionPerformed(ActionEvent e)
966 annotationColumn_actionPerformed(e);
970 JMenuItem createGroup = new JMenuItem(
971 MessageManager.getString("action.create_group"));
972 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
973 jalview.util.ShortcutKeyMaskExWrapper
974 .getMenuShortcutKeyMaskEx(),
976 al = new ActionListener()
979 public void actionPerformed(ActionEvent e)
981 createGroup_actionPerformed(e);
984 addMenuActionAndAccelerator(keyStroke, createGroup, al);
986 JMenuItem unGroup = new JMenuItem(
987 MessageManager.getString("action.remove_group"));
988 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
989 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
990 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
992 al = new ActionListener()
995 public void actionPerformed(ActionEvent e)
997 unGroup_actionPerformed(e);
1000 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1002 copy.setText(MessageManager.getString("action.copy"));
1003 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1004 jalview.util.ShortcutKeyMaskExWrapper
1005 .getMenuShortcutKeyMaskEx(),
1008 al = new ActionListener()
1011 public void actionPerformed(ActionEvent e)
1013 copy_actionPerformed();
1016 addMenuActionAndAccelerator(keyStroke, copy, al);
1018 cut.setText(MessageManager.getString("action.cut"));
1019 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1020 jalview.util.ShortcutKeyMaskExWrapper
1021 .getMenuShortcutKeyMaskEx(),
1023 al = new ActionListener()
1026 public void actionPerformed(ActionEvent e)
1028 cut_actionPerformed();
1031 addMenuActionAndAccelerator(keyStroke, cut, al);
1033 JMenuItem delete = new JMenuItem(
1034 MessageManager.getString("action.delete"));
1035 delete.addActionListener(new ActionListener()
1038 public void actionPerformed(ActionEvent e)
1040 delete_actionPerformed();
1044 pasteMenu.setText(MessageManager.getString("action.paste"));
1045 JMenuItem pasteNew = new JMenuItem(
1046 MessageManager.getString("label.to_new_alignment"));
1047 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1048 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1049 | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1051 al = new ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 pasteNew_actionPerformed(e);
1059 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1061 JMenuItem pasteThis = new JMenuItem(
1062 MessageManager.getString("label.to_this_alignment"));
1063 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1064 jalview.util.ShortcutKeyMaskExWrapper
1065 .getMenuShortcutKeyMaskEx(),
1067 al = new ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 pasteThis_actionPerformed(e);
1075 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1077 JMenuItem createPNG = new JMenuItem("PNG");
1078 createPNG.addActionListener(new ActionListener()
1081 public void actionPerformed(ActionEvent e)
1086 createPNG.setActionCommand(
1087 MessageManager.getString("label.save_png_image"));
1089 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1090 font.addActionListener(new ActionListener()
1093 public void actionPerformed(ActionEvent e)
1095 font_actionPerformed(e);
1099 MessageManager.getString("label.show_sequence_limits"));
1100 seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
1101 seqLimits.addActionListener(new ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 seqLimit_actionPerformed(e);
1109 JMenuItem epsFile = new JMenuItem("EPS");
1110 epsFile.addActionListener(new ActionListener()
1113 public void actionPerformed(ActionEvent e)
1119 JMenuItem createSVG = new JMenuItem("SVG");
1120 createSVG.addActionListener(new ActionListener()
1123 public void actionPerformed(ActionEvent e)
1129 JMenuItem loadTreeMenuItem = new JMenuItem(
1130 MessageManager.getString("label.load_associated_tree"));
1131 loadTreeMenuItem.setActionCommand(
1132 MessageManager.getString("label.load_tree_for_sequence_set"));
1133 loadTreeMenuItem.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 loadTreeMenuItem_actionPerformed(e);
1142 scaleAbove.setVisible(false);
1143 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1144 scaleAbove.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent e)
1149 scaleAbove_actionPerformed(e);
1152 scaleLeft.setVisible(false);
1153 scaleLeft.setSelected(true);
1154 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1155 scaleLeft.addActionListener(new ActionListener()
1158 public void actionPerformed(ActionEvent e)
1160 scaleLeft_actionPerformed(e);
1163 scaleRight.setVisible(false);
1164 scaleRight.setSelected(true);
1165 scaleRight.setText(MessageManager.getString("action.scale_right"));
1166 scaleRight.addActionListener(new ActionListener()
1169 public void actionPerformed(ActionEvent e)
1171 scaleRight_actionPerformed(e);
1174 centreColumnLabelsMenuItem.setVisible(true);
1175 centreColumnLabelsMenuItem.setState(false);
1176 centreColumnLabelsMenuItem.setText(
1177 MessageManager.getString("label.centre_column_labels"));
1178 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1181 public void actionPerformed(ActionEvent e)
1183 centreColumnLabels_actionPerformed(e);
1186 followHighlightMenuItem.setVisible(true);
1187 followHighlightMenuItem.setState(true);
1188 followHighlightMenuItem
1189 .setText(MessageManager.getString("label.automatic_scrolling"));
1190 followHighlightMenuItem.addActionListener(new ActionListener()
1194 public void actionPerformed(ActionEvent e)
1196 followHighlight_actionPerformed();
1202 .setText(MessageManager.getString("action.by_tree_order"));
1203 sort.setText(MessageManager.getString("action.sort"));
1204 sort.addMenuListener(new MenuListener()
1207 public void menuSelected(MenuEvent e)
1209 buildTreeSortMenu();
1213 public void menuDeselected(MenuEvent e)
1218 public void menuCanceled(MenuEvent e)
1223 .setText(MessageManager.getString("label.sort_by_score"));
1224 sort.add(sortByAnnotScore);
1225 sort.addMenuListener(new javax.swing.event.MenuListener()
1229 public void menuCanceled(MenuEvent e)
1234 public void menuDeselected(MenuEvent e)
1239 public void menuSelected(MenuEvent e)
1241 buildSortByAnnotationScoresMenu();
1244 sortByAnnotScore.setVisible(false);
1247 .setText(MessageManager.getString("action.calculate_tree_pca"));
1249 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1250 padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
1251 padGapsMenuitem.addActionListener(new ActionListener()
1254 public void actionPerformed(ActionEvent e)
1256 padGapsMenuitem_actionPerformed(e);
1259 JMenuItem vamsasStore = new JMenuItem(
1260 MessageManager.getString("label.vamsas_store"));
1261 vamsasStore.setVisible(false);
1262 vamsasStore.addActionListener(new ActionListener()
1265 public void actionPerformed(ActionEvent e)
1267 vamsasStore_actionPerformed(e);
1272 * Translate as cDNA with sub-menu of translation tables
1275 .setText(MessageManager.getString("label.translate_cDNA"));
1276 boolean first = true;
1277 for (final GeneticCodeI table : GeneticCodes.getInstance()
1280 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1281 showTranslation.add(item);
1282 item.addActionListener(new ActionListener()
1285 public void actionPerformed(ActionEvent e)
1287 showTranslation_actionPerformed(table);
1292 showTranslation.addSeparator();
1297 showReverse.setText(MessageManager.getString("label.reverse"));
1298 showReverse.addActionListener(new ActionListener()
1301 public void actionPerformed(ActionEvent e)
1303 showReverse_actionPerformed(false);
1306 showReverseComplement
1307 .setText(MessageManager.getString("label.reverse_complement"));
1308 showReverseComplement.addActionListener(new ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 showReverse_actionPerformed(true);
1317 JMenuItem extractScores = new JMenuItem(
1318 MessageManager.getString("label.extract_scores"));
1319 extractScores.addActionListener(new ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 extractScores_actionPerformed(e);
1327 extractScores.setVisible(true);
1328 // JBPNote: TODO: make gui for regex based score extraction
1330 // for show products actions see AlignFrame.canShowProducts
1331 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1333 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1334 runGroovy.setToolTipText(
1335 MessageManager.getString("label.run_groovy_tip"));
1336 runGroovy.addActionListener(new ActionListener()
1339 public void actionPerformed(ActionEvent e)
1341 runGroovy_actionPerformed();
1345 openFeatureSettings = new JMenuItem(
1346 MessageManager.getString("action.feature_settings"));
1347 openFeatureSettings.addActionListener(new ActionListener()
1350 public void actionPerformed(ActionEvent e)
1352 featureSettings_actionPerformed(e);
1357 * add sub-menu of database we can fetch from
1359 JMenuItem fetchSequence = new JMenuItem(
1360 MessageManager.getString("label.fetch_sequences"));
1361 fetchSequence.addActionListener(new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 fetchSequence_actionPerformed();
1370 JMenuItem associatedData = new JMenuItem(
1371 MessageManager.getString("label.load_features_annotations"));
1372 associatedData.addActionListener(new ActionListener()
1375 public void actionPerformed(ActionEvent e)
1377 associatedData_actionPerformed(e);
1380 loadVcf = new JMenuItem(
1381 MessageManager.getString("label.load_vcf_file"));
1382 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1383 loadVcf.addActionListener(new ActionListener()
1386 public void actionPerformed(ActionEvent e)
1388 loadVcf_actionPerformed();
1391 autoCalculate.setText(
1392 MessageManager.getString("label.autocalculate_consensus"));
1393 autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1394 autoCalculate.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 autoCalculate_actionPerformed(e);
1403 MessageManager.getString("label.sort_alignment_new_tree"));
1404 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1405 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1406 sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
1407 sortByTree.addActionListener(new ActionListener()
1410 public void actionPerformed(ActionEvent e)
1412 sortByTreeOption_actionPerformed(e);
1416 listenToViewSelections.setText(
1417 MessageManager.getString("label.listen_for_selections"));
1418 listenToViewSelections
1419 .setToolTipText("<html>" + MessageManager.getString(
1420 "label.selections_mirror_selections_made_same_sequences_other_views"));
1421 listenToViewSelections.setState(false);
1422 listenToViewSelections.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 listenToViewSelections_actionPerformed(e);
1431 JMenu addSequenceMenu = new JMenu(
1432 MessageManager.getString("label.add_sequences"));
1433 JMenuItem addFromFile = new JMenuItem(
1434 MessageManager.getString("label.from_file"));
1435 addFromFile.addActionListener(new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1440 addFromFile_actionPerformed(e);
1443 JMenuItem addFromText = new JMenuItem(
1444 MessageManager.getString("label.from_textbox"));
1445 addFromText.addActionListener(new ActionListener()
1448 public void actionPerformed(ActionEvent e)
1450 addFromText_actionPerformed(e);
1453 JMenuItem addFromURL = new JMenuItem(
1454 MessageManager.getString("label.from_url"));
1455 addFromURL.addActionListener(new ActionListener()
1458 public void actionPerformed(ActionEvent e)
1460 addFromURL_actionPerformed(e);
1463 JMenuItem exportFeatures = new JMenuItem(
1464 MessageManager.getString("label.export_features"));
1465 exportFeatures.addActionListener(new ActionListener()
1468 public void actionPerformed(ActionEvent e)
1470 exportFeatures_actionPerformed(e);
1473 JMenuItem exportAnnotations = new JMenuItem(
1474 MessageManager.getString("label.export_annotations"));
1475 exportAnnotations.addActionListener(new ActionListener()
1478 public void actionPerformed(ActionEvent e)
1480 exportAnnotations_actionPerformed(e);
1483 statusPanel.setLayout(new GridLayout());
1484 JMenuItem showAllSeqs = new JMenuItem(
1485 MessageManager.getString("label.all_sequences"));
1486 showAllSeqs.setToolTipText(
1487 MessageManager.getString("label.toggle_sequence_visibility"));
1488 showAllSeqs.addActionListener(new ActionListener()
1491 public void actionPerformed(ActionEvent e)
1493 showAllSeqs_actionPerformed(e);
1496 JMenuItem showAllColumns = new JMenuItem(
1497 MessageManager.getString("label.all_columns"));
1498 showAllColumns.setToolTipText(
1499 MessageManager.getString("label.toggle_columns_visibility"));
1500 showAllColumns.addActionListener(new ActionListener()
1503 public void actionPerformed(ActionEvent e)
1505 showAllColumns_actionPerformed(e);
1508 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1509 JMenuItem hideSelSequences = new JMenuItem(
1510 MessageManager.getString("label.selected_sequences"));
1511 hideSelSequences.setToolTipText(
1512 MessageManager.getString("label.toggle_sequence_visibility"));
1513 hideSelSequences.addActionListener(new ActionListener()
1516 public void actionPerformed(ActionEvent e)
1518 hideSelSequences_actionPerformed(e);
1521 JMenuItem hideSelColumns = new JMenuItem(
1522 MessageManager.getString("label.selected_columns"));
1523 hideSelColumns.setToolTipText(
1524 MessageManager.getString("label.toggle_columns_visibility"));
1525 hideSelColumns.addActionListener(new ActionListener()
1528 public void actionPerformed(ActionEvent e)
1530 hideSelColumns_actionPerformed(e);
1533 JMenuItem hideAllSelection = new JMenuItem(
1534 MessageManager.getString("label.selected_region"));
1535 hideAllSelection.addActionListener(new ActionListener()
1538 public void actionPerformed(ActionEvent e)
1540 hideAllSelection_actionPerformed(e);
1543 // TODO: should be hidden if no selection exists.
1544 JMenuItem hideAllButSelection = new JMenuItem(
1545 MessageManager.getString("label.all_but_selected_region"));
1546 hideAllButSelection.addActionListener(new ActionListener()
1549 public void actionPerformed(ActionEvent e)
1551 hideAllButSelection_actionPerformed(e);
1554 JMenuItem showAllhidden = new JMenuItem(
1555 MessageManager.getString("label.all_sequences_columns"));
1556 showAllhidden.setToolTipText(MessageManager
1557 .getString("label.toggles_visibility_hidden_selected_regions"));
1558 showAllhidden.addActionListener(new ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 showAllhidden_actionPerformed(e);
1566 hiddenMarkers.setText(
1567 MessageManager.getString("action.show_hidden_markers"));
1568 hiddenMarkers.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 hiddenMarkers_actionPerformed(e);
1577 JMenuItem invertColSel = new JMenuItem(
1578 MessageManager.getString("action.invert_column_selection"));
1579 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1580 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1581 | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
1583 al = new ActionListener()
1586 public void actionPerformed(ActionEvent e)
1588 invertColSel_actionPerformed(e);
1591 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1593 showComplementMenuItem.setVisible(false);
1594 showComplementMenuItem.addActionListener(new ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 showComplement_actionPerformed(showComplementMenuItem.getState());
1603 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1606 public void stateChanged(ChangeEvent evt)
1608 JTabbedPane pane = (JTabbedPane) evt.getSource();
1609 int sel = pane.getSelectedIndex();
1610 tabSelectionChanged(sel);
1613 tabbedPane.addMouseListener(new MouseAdapter()
1616 public void mousePressed(MouseEvent e)
1618 if (e.isPopupTrigger()) // Mac
1620 tabbedPane_mousePressed(e);
1625 public void mouseReleased(MouseEvent e)
1627 if (e.isPopupTrigger()) // Windows
1629 tabbedPane_mousePressed(e);
1633 tabbedPane.addFocusListener(new FocusAdapter()
1636 public void focusGained(FocusEvent e)
1638 tabbedPane_focusGained(e);
1642 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1643 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1644 jalview.util.ShortcutKeyMaskExWrapper
1645 .getMenuShortcutKeyMaskEx(),
1647 al = new ActionListener()
1650 public void actionPerformed(ActionEvent e)
1652 save_actionPerformed(e);
1655 addMenuActionAndAccelerator(keyStroke, save, al);
1657 reload.setEnabled(false);
1658 reload.setText(MessageManager.getString("action.reload"));
1659 reload.addActionListener(new ActionListener()
1662 public void actionPerformed(ActionEvent e)
1664 reload_actionPerformed(e);
1668 JMenuItem newView = new JMenuItem(
1669 MessageManager.getString("action.new_view"));
1670 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1671 jalview.util.ShortcutKeyMaskExWrapper
1672 .getMenuShortcutKeyMaskEx(),
1674 al = new ActionListener()
1677 public void actionPerformed(ActionEvent e)
1679 newView_actionPerformed(e);
1682 addMenuActionAndAccelerator(keyStroke, newView, al);
1684 tabbedPane.setToolTipText("<html><i>"
1685 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1688 formatMenu.setText(MessageManager.getString("action.format"));
1689 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1691 idRightAlign.setText(
1692 MessageManager.getString("label.right_align_sequence_id"));
1693 idRightAlign.addActionListener(new ActionListener()
1696 public void actionPerformed(ActionEvent e)
1698 idRightAlign_actionPerformed(e);
1702 gatherViews.setEnabled(false);
1703 gatherViews.setText(MessageManager.getString("action.gather_views"));
1704 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1705 al = new ActionListener()
1708 public void actionPerformed(ActionEvent e)
1710 gatherViews_actionPerformed(e);
1713 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1715 expandViews.setEnabled(false);
1716 expandViews.setText(MessageManager.getString("action.expand_views"));
1717 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1718 al = new ActionListener()
1721 public void actionPerformed(ActionEvent e)
1723 expandViews_actionPerformed(e);
1726 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1728 JMenuItem pageSetup = new JMenuItem(
1729 MessageManager.getString("action.page_setup"));
1730 pageSetup.addActionListener(new ActionListener()
1733 public void actionPerformed(ActionEvent e)
1735 pageSetup_actionPerformed(e);
1738 JMenuItem alignmentProperties = new JMenuItem(
1739 MessageManager.getString("label.alignment_props"));
1740 alignmentProperties.addActionListener(new ActionListener()
1743 public void actionPerformed(ActionEvent actionEvent)
1745 alignmentProperties();
1748 JMenuItem selectHighlighted = new JMenuItem(
1749 MessageManager.getString("action.select_highlighted_columns"));
1750 selectHighlighted.setToolTipText(
1751 MessageManager.getString("tooltip.select_highlighted_columns"));
1752 al = new ActionListener()
1755 public void actionPerformed(ActionEvent actionEvent)
1757 selectHighlightedColumns_actionPerformed(actionEvent);
1760 selectHighlighted.addActionListener(al);
1762 copyHighlighted = new JMenuItem(
1763 MessageManager.getString("action.copy_highlighted_regions"));
1764 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1765 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
1766 + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
1768 copyHighlighted.setToolTipText(
1769 MessageManager.getString("tooltip.copy_highlighted_regions"));
1770 al = new ActionListener()
1773 public void actionPerformed(ActionEvent actionEvent)
1775 copyHighlightedColumns_actionPerformed(actionEvent);
1778 addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
1779 copyHighlighted.addActionListener(al);
1781 JMenu tooltipSettingsMenu = new JMenu(
1782 MessageManager.getString("label.sequence_id_tooltip"));
1783 JMenu autoAnnMenu = new JMenu(
1784 MessageManager.getString("label.autocalculated_annotation"));
1786 JMenu exportImageMenu = new JMenu(
1787 MessageManager.getString("label.export_image"));
1788 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1789 alignFrameMenuBar.add(fileMenu);
1790 alignFrameMenuBar.add(editMenu);
1791 alignFrameMenuBar.add(selectMenu);
1792 alignFrameMenuBar.add(viewMenu);
1793 alignFrameMenuBar.add(annotationsMenu);
1794 alignFrameMenuBar.add(formatMenu);
1795 alignFrameMenuBar.add(colourMenu);
1796 alignFrameMenuBar.add(calculateMenu);
1797 if (!Platform.isJS())
1799 alignFrameMenuBar.add(webService);
1802 fileMenu.add(fetchSequence);
1803 fileMenu.add(addSequenceMenu);
1804 fileMenu.add(reload);
1805 fileMenu.addSeparator();
1806 fileMenu.add(vamsasStore);
1808 fileMenu.add(saveAs);
1809 fileMenu.add(outputTextboxMenu);
1810 fileMenu.add(pageSetup);
1811 fileMenu.add(printMenuItem);
1812 fileMenu.addSeparator();
1813 fileMenu.add(exportImageMenu);
1814 fileMenu.add(exportFeatures);
1815 fileMenu.add(exportAnnotations);
1816 fileMenu.add(loadTreeMenuItem);
1817 fileMenu.add(associatedData);
1818 if (!Platform.isJS())
1820 fileMenu.add(loadVcf);
1822 fileMenu.addSeparator();
1823 fileMenu.add(closeMenuItem);
1825 pasteMenu.add(pasteNew);
1826 pasteMenu.add(pasteThis);
1827 editMenu.add(undoMenuItem);
1828 editMenu.add(redoMenuItem);
1831 editMenu.add(copyHighlighted);
1832 editMenu.add(pasteMenu);
1833 editMenu.add(delete);
1834 editMenu.addSeparator();
1835 editMenu.add(remove2LeftMenuItem);
1836 editMenu.add(remove2RightMenuItem);
1837 editMenu.add(removeGappedColumnMenuItem);
1838 editMenu.add(removeAllGapsMenuItem);
1839 editMenu.add(removeRedundancyMenuItem);
1840 editMenu.addSeparator();
1841 // dont add these yet in the CVS build - they cannot be undone!
1842 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1843 // editMenu.add(justifyLeftMenuItem);
1844 // editMenu.add(justifyRightMenuItem);
1845 // editMenu.addSeparator();
1846 editMenu.add(padGapsMenuitem);
1848 showMenu.add(showAllColumns);
1849 showMenu.add(showAllSeqs);
1850 showMenu.add(showAllhidden);
1851 hideMenu.add(hideSelColumns);
1852 hideMenu.add(hideSelSequences);
1853 hideMenu.add(hideAllSelection);
1854 hideMenu.add(hideAllButSelection);
1855 viewMenu.add(newView);
1856 viewMenu.add(expandViews);
1857 viewMenu.add(gatherViews);
1858 viewMenu.addSeparator();
1859 viewMenu.add(showMenu);
1860 viewMenu.add(hideMenu);
1861 viewMenu.add(showComplementMenuItem);
1862 viewMenu.addSeparator();
1863 viewMenu.add(followHighlightMenuItem);
1864 viewMenu.addSeparator();
1865 viewMenu.add(showSeqFeatures);
1866 // viewMenu.add(showSeqFeaturesHeight);
1867 viewMenu.add(openFeatureSettings);
1868 tooltipSettingsMenu.add(showDbRefsMenuitem);
1869 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1870 viewMenu.add(tooltipSettingsMenu);
1871 viewMenu.addSeparator();
1872 viewMenu.add(alignmentProperties);
1873 viewMenu.addSeparator();
1874 viewMenu.add(overviewMenuItem);
1876 annotationsMenu.add(annotationPanelMenuItem);
1877 annotationsMenu.addSeparator();
1878 annotationsMenu.add(showAllAlAnnotations);
1879 annotationsMenu.add(hideAllAlAnnotations);
1880 annotationsMenu.addSeparator();
1881 annotationsMenu.add(showAllSeqAnnotations);
1882 annotationsMenu.add(hideAllSeqAnnotations);
1883 annotationsMenu.add(sortAnnBySequence);
1884 annotationsMenu.add(sortAnnByLabel);
1885 annotationsMenu.addSeparator();
1886 autoAnnMenu.add(showAutoFirst);
1887 autoAnnMenu.add(showAutoLast);
1888 autoAnnMenu.addSeparator();
1889 autoAnnMenu.add(applyAutoAnnotationSettings);
1890 autoAnnMenu.add(showConsensusHistogram);
1891 autoAnnMenu.add(showSequenceLogo);
1892 autoAnnMenu.add(normaliseSequenceLogo);
1893 autoAnnMenu.addSeparator();
1894 autoAnnMenu.add(showGroupConservation);
1895 autoAnnMenu.add(showGroupConsensus);
1896 annotationsMenu.add(autoAnnMenu);
1898 sort.add(sortIDMenuItem);
1899 sort.add(sortLengthMenuItem);
1900 sort.add(sortGroupMenuItem);
1901 sort.add(sortPairwiseMenuItem);
1902 sort.add(sortByTreeMenu);
1903 calculateMenu.add(sort);
1904 calculateMenu.add(calculateTree);
1905 calculateMenu.addSeparator();
1906 calculateMenu.add(pairwiseAlignmentMenuItem);
1907 calculateMenu.addSeparator();
1908 calculateMenu.add(showTranslation);
1909 calculateMenu.add(showReverse);
1910 calculateMenu.add(showReverseComplement);
1911 calculateMenu.add(showProducts);
1912 calculateMenu.add(autoCalculate);
1913 calculateMenu.add(sortByTree);
1914 calculateMenu.addSeparator();
1915 calculateMenu.add(expandAlignment);
1916 calculateMenu.add(extractScores);
1917 if (!Platform.isJS())
1919 calculateMenu.addSeparator();
1920 calculateMenu.add(runGroovy);
1923 webServiceNoServices = new JMenuItem(
1924 MessageManager.getString("label.no_services"));
1925 webService.add(webServiceNoServices);
1926 if (!Platform.isJS())
1928 exportImageMenu.add(htmlMenuItem);
1930 exportImageMenu.add(epsFile);
1931 exportImageMenu.add(createPNG);
1932 if (!Platform.isJS())
1934 exportImageMenu.add(createBioJS);
1935 exportImageMenu.add(createSVG);
1937 addSequenceMenu.add(addFromFile);
1938 addSequenceMenu.add(addFromText);
1939 addSequenceMenu.add(addFromURL);
1940 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1941 statusPanel.add(statusBar, null);
1942 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1944 formatMenu.add(font);
1945 formatMenu.addSeparator();
1946 formatMenu.add(wrapMenuItem);
1947 formatMenu.add(scaleAbove);
1948 formatMenu.add(scaleLeft);
1949 formatMenu.add(scaleRight);
1950 formatMenu.add(seqLimits);
1951 formatMenu.add(idRightAlign);
1952 formatMenu.add(hiddenMarkers);
1953 formatMenu.add(viewBoxesMenuItem);
1954 formatMenu.add(viewTextMenuItem);
1955 formatMenu.add(colourTextMenuItem);
1956 formatMenu.add(renderGapsMenuItem);
1957 formatMenu.add(centreColumnLabelsMenuItem);
1958 formatMenu.add(showNonconservedMenuItem);
1959 selectMenu.add(findMenuItem);
1960 selectMenu.addSeparator();
1961 selectMenu.add(selectAllSequenceMenuItem);
1962 selectMenu.add(deselectAllSequenceMenuItem);
1963 selectMenu.add(invertSequenceMenuItem);
1964 selectMenu.add(invertColSel);
1965 selectMenu.add(createGroup);
1966 selectMenu.add(unGroup);
1967 selectMenu.add(grpsFromSelection);
1968 selectMenu.add(deleteGroups);
1969 selectMenu.add(annotationColumn);
1970 selectMenu.add(selectHighlighted);
1971 // TODO - determine if the listenToViewSelections button is needed : see bug
1973 // selectMenu.addSeparator();
1974 // selectMenu.add(listenToViewSelections);
1977 protected void copyHighlightedColumns_actionPerformed(
1978 ActionEvent actionEvent)
1983 protected void loadVcf_actionPerformed()
1988 * Constructs the entries on the Colour menu (but does not add them to the
1991 protected void initColourMenu()
1993 applyToAllGroups = new JCheckBoxMenuItem(
1994 MessageManager.getString("label.apply_colour_to_all_groups"));
1995 applyToAllGroups.addActionListener(new ActionListener()
1998 public void actionPerformed(ActionEvent e)
2000 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2004 textColour = new JMenuItem(
2005 MessageManager.getString("label.text_colour"));
2006 textColour.addActionListener(new ActionListener()
2009 public void actionPerformed(ActionEvent e)
2011 textColour_actionPerformed();
2015 conservationMenuItem = new JCheckBoxMenuItem(
2016 MessageManager.getString("action.by_conservation"));
2017 conservationMenuItem.addActionListener(new ActionListener()
2020 public void actionPerformed(ActionEvent e)
2022 conservationMenuItem_actionPerformed(
2023 conservationMenuItem.isSelected());
2027 abovePIDThreshold = new JCheckBoxMenuItem(
2028 MessageManager.getString("label.above_identity_threshold"));
2029 abovePIDThreshold.addActionListener(new ActionListener()
2032 public void actionPerformed(ActionEvent e)
2034 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2037 modifyPID = new JMenuItem(
2038 MessageManager.getString("label.modify_identity_threshold"));
2039 modifyPID.addActionListener(new ActionListener()
2042 public void actionPerformed(ActionEvent e)
2044 modifyPID_actionPerformed();
2047 modifyConservation = new JMenuItem(MessageManager
2048 .getString("label.modify_conservation_threshold"));
2049 modifyConservation.addActionListener(new ActionListener()
2052 public void actionPerformed(ActionEvent e)
2054 modifyConservation_actionPerformed();
2058 annotationColour = new JRadioButtonMenuItem(
2059 MessageManager.getString("action.by_annotation"));
2060 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
2061 annotationColour.addActionListener(new ActionListener()
2064 public void actionPerformed(ActionEvent e)
2066 annotationColour_actionPerformed();
2071 protected void selectHighlightedColumns_actionPerformed(
2072 ActionEvent actionEvent)
2074 // TODO Auto-generated method stub
2079 * Generate the reverse sequence (or reverse complement if the flag is true)
2080 * and add it to the alignment
2084 protected void showReverse_actionPerformed(boolean complement)
2089 * Try to run script in a Groovy console, having first ensured that this
2090 * alignframe is set as currentAlignFrame in Desktop
2092 protected void runGroovy_actionPerformed()
2098 * Adds the given action listener and key accelerator to the given menu item.
2099 * Also saves in a lookup table to support lookup of action by key stroke.
2103 * @param actionListener
2105 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2106 JMenuItem menuItem, ActionListener actionListener)
2108 menuItem.setAccelerator(keyStroke);
2109 accelerators.put(keyStroke, menuItem);
2110 menuItem.addActionListener(actionListener);
2114 * Action on clicking sort annotations by type.
2118 protected void sortAnnotations_actionPerformed()
2123 * Action on clicking Show all annotations.
2125 * @param forSequences
2126 * update sequence-related annotations
2127 * @param forAlignment
2128 * update non-sequence-related annotations
2130 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2131 boolean forAlignment)
2133 setAnnotationsVisibility(true, forSequences, forAlignment);
2137 * Action on clicking Hide all annotations.
2139 * @param forSequences
2140 * update sequence-related annotations
2141 * @param forAlignment
2142 * update non-sequence-related annotations
2144 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2145 boolean forAlignment)
2147 setAnnotationsVisibility(false, forSequences, forAlignment);
2151 * Set the visibility of annotations to true or false. Can act on
2152 * sequence-related annotations, or alignment-related, or both.
2155 * @param forSequences
2156 * update sequence-related annotations
2157 * @param forAlignment
2158 * update non-sequence-related annotations
2160 protected void setAnnotationsVisibility(boolean visible,
2161 boolean forSequences, boolean forAlignment)
2166 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2168 // TODO Auto-generated method stub
2172 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2174 // TODO Auto-generated method stub
2178 protected void showAllhidden_actionPerformed(ActionEvent e)
2180 // TODO Auto-generated method stub
2184 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2186 // TODO Auto-generated method stub
2190 protected void hideAllSelection_actionPerformed(ActionEvent e)
2192 // TODO Auto-generated method stub
2196 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2198 // TODO Auto-generated method stub
2202 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2204 // TODO Auto-generated method stub
2208 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2210 // TODO Auto-generated method stub
2214 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2216 // TODO Auto-generated method stub
2220 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2222 // TODO Auto-generated method stub
2226 protected void showGroupConservation_actionPerformed(ActionEvent e)
2228 // TODO Auto-generated method stub
2232 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2234 // TODO Auto-generated method stub
2238 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2240 // TODO Auto-generated method stub
2244 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2246 // TODO Auto-generated method stub
2250 protected void followHighlight_actionPerformed()
2252 // TODO Auto-generated method stub
2256 protected void showNpFeats_actionPerformed(ActionEvent e)
2258 // TODO Auto-generated method stub
2262 protected void showDbRefs_actionPerformed(ActionEvent e)
2264 // TODO Auto-generated method stub
2268 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2272 protected void buildSortByAnnotationScoresMenu()
2276 protected void extractScores_actionPerformed(ActionEvent e)
2280 protected void outputText_actionPerformed(String formatName)
2284 public void addFromFile_actionPerformed(ActionEvent e)
2289 public void addFromText_actionPerformed(ActionEvent e)
2294 public void addFromURL_actionPerformed(ActionEvent e)
2299 public void exportFeatures_actionPerformed(ActionEvent e)
2304 public void exportAnnotations_actionPerformed(ActionEvent e)
2309 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2313 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2318 protected void closeMenuItem_actionPerformed(boolean b)
2322 protected void redoMenuItem_actionPerformed(ActionEvent e)
2326 protected void undoMenuItem_actionPerformed(ActionEvent e)
2330 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2334 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2338 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2342 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2346 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2350 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2354 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2358 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2362 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2366 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2370 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2374 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2378 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2382 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2386 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2390 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2394 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2398 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2402 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2406 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2410 protected void conservationMenuItem_actionPerformed(boolean selected)
2414 protected void printMenuItem_actionPerformed(ActionEvent e)
2418 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2422 protected void findMenuItem_actionPerformed(ActionEvent e)
2426 protected void abovePIDThreshold_actionPerformed(boolean selected)
2430 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2434 protected void deleteGroups_actionPerformed(ActionEvent e)
2438 protected void createGroup_actionPerformed(ActionEvent e)
2442 protected void unGroup_actionPerformed(ActionEvent e)
2446 protected void copy_actionPerformed()
2450 protected void cut_actionPerformed()
2454 protected void delete_actionPerformed()
2458 protected void pasteNew_actionPerformed(ActionEvent e)
2462 protected void pasteThis_actionPerformed(ActionEvent e)
2466 protected void applyToAllGroups_actionPerformed(boolean selected)
2470 public void createPNG(java.io.File f)
2474 protected void font_actionPerformed(ActionEvent e)
2478 protected void seqLimit_actionPerformed(ActionEvent e)
2482 public void seqDBRef_actionPerformed(ActionEvent e)
2487 public void createEPS(java.io.File f)
2491 public void createSVG(java.io.File f)
2496 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2502 * Template method to handle the 'load T-Coffee scores' menu event.
2504 * Subclasses override this method to provide a custom action.
2509 protected void loadScores_actionPerformed(ActionEvent event)
2514 protected void jpred_actionPerformed(ActionEvent e)
2518 protected void scaleAbove_actionPerformed(ActionEvent e)
2522 protected void scaleLeft_actionPerformed(ActionEvent e)
2526 protected void scaleRight_actionPerformed(ActionEvent e)
2530 protected void modifyPID_actionPerformed()
2534 protected void modifyConservation_actionPerformed()
2538 protected void saveAs_actionPerformed()
2542 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2546 public void vamsasStore_actionPerformed(ActionEvent e)
2551 public void vamsasLoad_actionPerformed(ActionEvent e)
2556 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2561 public void featureSettings_actionPerformed(ActionEvent e)
2566 public void fetchSequence_actionPerformed()
2571 public void smoothFont_actionPerformed(ActionEvent e)
2576 public void annotationColour_actionPerformed()
2580 public void annotationColumn_actionPerformed(ActionEvent e)
2584 public void associatedData_actionPerformed(ActionEvent e)
2589 public void autoCalculate_actionPerformed(ActionEvent e)
2594 public void sortByTreeOption_actionPerformed(ActionEvent e)
2599 public void showAllSeqs_actionPerformed(ActionEvent e)
2604 public void showAllColumns_actionPerformed(ActionEvent e)
2609 public void hideSelSequences_actionPerformed(ActionEvent e)
2614 public void hideSelColumns_actionPerformed(ActionEvent e)
2619 public void hiddenMarkers_actionPerformed(ActionEvent e)
2624 public void findPdbId_actionPerformed(ActionEvent e)
2629 public void enterPdbId_actionPerformed(ActionEvent e)
2634 public void pdbFile_actionPerformed(ActionEvent e)
2639 public void invertColSel_actionPerformed(ActionEvent e)
2644 public void tabSelectionChanged(int sel)
2649 public void tabbedPane_mousePressed(MouseEvent e)
2654 public void tabbedPane_focusGained(FocusEvent e)
2659 public void save_actionPerformed(ActionEvent e)
2664 public void reload_actionPerformed(ActionEvent e)
2669 public void newView_actionPerformed(ActionEvent e)
2674 public void textColour_actionPerformed()
2679 public void idRightAlign_actionPerformed(ActionEvent e)
2684 public void expandViews_actionPerformed(ActionEvent e)
2689 public void gatherViews_actionPerformed(ActionEvent e)
2694 public void buildTreeSortMenu()
2699 public void pageSetup_actionPerformed(ActionEvent e)
2704 public void alignmentProperties()
2709 protected void expand_newalign(ActionEvent e)
2711 // TODO Auto-generated method stub
2715 protected boolean isShowAutoCalculatedAbove()
2717 return showAutoCalculatedAbove;
2720 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2722 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2725 protected SequenceAnnotationOrder getAnnotationSortOrder()
2727 return annotationSortOrder;
2730 protected void setAnnotationSortOrder(
2731 SequenceAnnotationOrder annotationSortOrder)
2733 this.annotationSortOrder = annotationSortOrder;
2736 public Map<KeyStroke, JMenuItem> getAccelerators()
2738 return this.accelerators;
2742 * Returns the selected index of the tabbed pane, or -1 if none selected
2743 * (including the case where the tabbed pane has not been made visible).
2747 public int getTabIndex()
2749 return tabbedPane.getSelectedIndex();
2752 public JPanel getStatusPanel()
2758 * Sets a reference to the containing split frame. Also makes the 'toggle
2759 * split view' menu item visible and checked.
2763 public void setSplitFrame(SplitContainerI sf)
2765 this.splitFrame = sf;
2768 this.showComplementMenuItem.setVisible(true);
2769 this.showComplementMenuItem.setState(true);
2773 public SplitContainerI getSplitViewContainer()
2775 return this.splitFrame;
2778 protected void showComplement_actionPerformed(boolean complement)