2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.analysis.GeneticCodeI;
25 import jalview.analysis.GeneticCodes;
26 import jalview.api.SplitContainerI;
27 import jalview.bin.Cache;
28 import jalview.gui.JvSwingUtils;
29 import jalview.gui.Preferences;
30 import jalview.io.FileFormats;
31 import jalview.schemes.ResidueColourScheme;
32 import jalview.util.MessageManager;
33 import jalview.util.Platform;
35 import java.awt.BorderLayout;
36 import java.awt.Color;
37 import java.awt.GridLayout;
38 import java.awt.Toolkit;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.awt.event.FocusAdapter;
42 import java.awt.event.FocusEvent;
43 import java.awt.event.KeyEvent;
44 import java.awt.event.MouseAdapter;
45 import java.awt.event.MouseEvent;
46 import java.util.HashMap;
49 import javax.swing.BorderFactory;
50 import javax.swing.ButtonGroup;
51 import javax.swing.JCheckBoxMenuItem;
52 import javax.swing.JInternalFrame;
53 import javax.swing.JLabel;
54 import javax.swing.JMenu;
55 import javax.swing.JMenuBar;
56 import javax.swing.JMenuItem;
57 import javax.swing.JPanel;
58 import javax.swing.JRadioButtonMenuItem;
59 import javax.swing.JTabbedPane;
60 import javax.swing.KeyStroke;
61 import javax.swing.event.ChangeEvent;
62 import javax.swing.event.MenuEvent;
63 import javax.swing.event.MenuListener;
65 public class GAlignFrame extends JInternalFrame
67 protected JMenuBar alignFrameMenuBar = new JMenuBar();
69 protected JMenuItem closeMenuItem = new JMenuItem();
71 protected JMenu webService = new JMenu();
73 protected JMenuItem webServiceNoServices;
75 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
77 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
79 protected JMenu sortByAnnotScore = new JMenu();
81 protected JLabel statusBar = new JLabel();
83 protected JMenu outputTextboxMenu = new JMenu();
85 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
87 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
89 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
91 protected JMenuItem undoMenuItem = new JMenuItem();
93 protected JMenuItem redoMenuItem = new JMenuItem();
95 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
97 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
99 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
101 JMenuItem copy = new JMenuItem();
103 JMenuItem cut = new JMenuItem();
105 JMenu pasteMenu = new JMenu();
107 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
109 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
111 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
113 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
115 protected JCheckBoxMenuItem applyToAllGroups;
117 protected JMenu colourMenu = new JMenu();
119 protected JMenuItem textColour;
121 protected JCheckBoxMenuItem conservationMenuItem;
123 protected JMenuItem modifyConservation;
125 protected JCheckBoxMenuItem abovePIDThreshold;
127 protected JMenuItem modifyPID;
129 protected JRadioButtonMenuItem annotationColour;
131 protected JMenu sortByTreeMenu = new JMenu();
133 protected JMenu sort = new JMenu();
135 protected JMenuItem calculateTree = new JMenuItem();
137 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
139 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
141 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
143 protected JMenu showTranslation = new JMenu();
145 protected JMenuItem showReverse = new JMenuItem();
147 protected JMenuItem showReverseComplement = new JMenuItem();
149 protected JMenu showProducts = new JMenu();
151 protected JMenuItem runGroovy = new JMenuItem();
153 protected JMenuItem loadVcf;
155 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
157 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
159 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
161 protected JPanel statusPanel = new JPanel();
163 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
165 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
167 protected JMenuItem showAllAlAnnotations = new JMenuItem();
169 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
171 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
173 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
175 protected JTabbedPane tabbedPane = new JTabbedPane();
177 protected JMenuItem reload = new JMenuItem();
179 protected JMenu formatMenu = new JMenu();
181 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
183 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
185 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
187 protected JMenuItem gatherViews = new JMenuItem();
189 protected JMenuItem expandViews = new JMenuItem();
191 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
193 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
203 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
205 private SplitContainerI splitFrame;
207 protected JMenuItem sortAnnBySequence;
209 protected JMenuItem sortAnnByLabel;
211 protected JMenu annotationsMenu;
218 setJMenuBar(alignFrameMenuBar);
220 // dynamically fill save as menu with available formats
221 for (String ff : FileFormats.getInstance().getWritableFormats(true))
223 JMenuItem item = new JMenuItem(ff);
225 item.addActionListener(new ActionListener()
228 public void actionPerformed(ActionEvent e)
230 outputText_actionPerformed(e);
234 outputTextboxMenu.add(item);
236 } catch (Exception e)
238 System.err.println(e.toString());
241 if (!Platform.isAMac())
243 closeMenuItem.setMnemonic('C');
244 outputTextboxMenu.setMnemonic('T');
245 undoMenuItem.setMnemonic('Z');
246 redoMenuItem.setMnemonic('0');
247 copy.setMnemonic('C');
248 cut.setMnemonic('U');
249 pasteMenu.setMnemonic('P');
250 reload.setMnemonic('R');
254 private void jbInit() throws Exception
258 JMenuItem saveAs = new JMenuItem(
259 MessageManager.getString("action.save_as"));
260 ActionListener al = new ActionListener()
263 public void actionPerformed(ActionEvent e)
265 saveAs_actionPerformed(e);
269 // FIXME getDefaultToolkit throws an exception in Headless mode
270 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
271 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
272 | KeyEvent.SHIFT_MASK,
274 addMenuActionAndAccelerator(keyStroke, saveAs, al);
276 closeMenuItem.setText(MessageManager.getString("action.close"));
277 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
278 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
279 al = new ActionListener()
282 public void actionPerformed(ActionEvent e)
284 closeMenuItem_actionPerformed(false);
287 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
289 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
290 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
291 annotationsMenu = new JMenu(
292 MessageManager.getString("action.annotations"));
293 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
294 colourMenu.setText(MessageManager.getString("action.colour"));
295 JMenu calculateMenu = new JMenu(
296 MessageManager.getString("action.calculate"));
297 webService.setText(MessageManager.getString("action.web_service"));
298 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
299 MessageManager.getString("action.select_all"));
300 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
301 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
302 al = new ActionListener()
305 public void actionPerformed(ActionEvent e)
307 selectAllSequenceMenuItem_actionPerformed(e);
310 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
312 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
313 MessageManager.getString("action.deselect_all"));
314 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
315 al = new ActionListener()
318 public void actionPerformed(ActionEvent e)
320 deselectAllSequenceMenuItem_actionPerformed(e);
323 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
325 JMenuItem invertSequenceMenuItem = new JMenuItem(
326 MessageManager.getString("action.invert_sequence_selection"));
327 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
328 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
329 al = new ActionListener()
332 public void actionPerformed(ActionEvent e)
334 invertSequenceMenuItem_actionPerformed(e);
337 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
339 JMenuItem grpsFromSelection = new JMenuItem(
340 MessageManager.getString("action.make_groups_selection"));
341 grpsFromSelection.addActionListener(new ActionListener()
344 public void actionPerformed(ActionEvent e)
346 makeGrpsFromSelection_actionPerformed(e);
349 JMenuItem expandAlignment = new JMenuItem(
350 MessageManager.getString("action.view_flanking_regions"));
351 expandAlignment.setToolTipText(
352 MessageManager.getString("label.view_flanking_regions"));
353 expandAlignment.addActionListener(new ActionListener()
356 public void actionPerformed(ActionEvent e)
361 JMenuItem remove2LeftMenuItem = new JMenuItem(
362 MessageManager.getString("action.remove_left"));
363 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
364 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
365 al = new ActionListener()
368 public void actionPerformed(ActionEvent e)
370 remove2LeftMenuItem_actionPerformed(e);
373 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
375 JMenuItem remove2RightMenuItem = new JMenuItem(
376 MessageManager.getString("action.remove_right"));
377 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
378 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
379 al = new ActionListener()
382 public void actionPerformed(ActionEvent e)
384 remove2RightMenuItem_actionPerformed(e);
387 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
389 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
390 MessageManager.getString("action.remove_empty_columns"));
391 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
392 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
393 al = new ActionListener()
396 public void actionPerformed(ActionEvent e)
398 removeGappedColumnMenuItem_actionPerformed(e);
401 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
403 JMenuItem removeAllGapsMenuItem = new JMenuItem(
404 MessageManager.getString("action.remove_all_gaps"));
405 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
406 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
407 | KeyEvent.SHIFT_MASK,
409 al = new ActionListener()
412 public void actionPerformed(ActionEvent e)
414 removeAllGapsMenuItem_actionPerformed(e);
417 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
419 JMenuItem justifyLeftMenuItem = new JMenuItem(
420 MessageManager.getString("action.left_justify_alignment"));
421 justifyLeftMenuItem.addActionListener(new ActionListener()
424 public void actionPerformed(ActionEvent e)
426 justifyLeftMenuItem_actionPerformed(e);
429 JMenuItem justifyRightMenuItem = new JMenuItem(
430 MessageManager.getString("action.right_justify_alignment"));
431 justifyRightMenuItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent e)
436 justifyRightMenuItem_actionPerformed(e);
439 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
440 viewBoxesMenuItem.setState(true);
441 viewBoxesMenuItem.addActionListener(new ActionListener()
444 public void actionPerformed(ActionEvent e)
446 viewBoxesMenuItem_actionPerformed(e);
449 viewTextMenuItem.setText(MessageManager.getString("action.text"));
450 viewTextMenuItem.setState(true);
451 viewTextMenuItem.addActionListener(new ActionListener()
454 public void actionPerformed(ActionEvent e)
456 viewTextMenuItem_actionPerformed(e);
459 showNonconservedMenuItem
460 .setText(MessageManager.getString("label.show_non_conserved"));
461 showNonconservedMenuItem.setState(false);
462 showNonconservedMenuItem.addActionListener(new ActionListener()
465 public void actionPerformed(ActionEvent e)
467 showUnconservedMenuItem_actionPerformed(e);
470 JMenuItem sortPairwiseMenuItem = new JMenuItem(
471 MessageManager.getString("action.by_pairwise_id"));
472 sortPairwiseMenuItem.addActionListener(new ActionListener()
475 public void actionPerformed(ActionEvent e)
477 sortPairwiseMenuItem_actionPerformed(e);
480 JMenuItem sortIDMenuItem = new JMenuItem(
481 MessageManager.getString("action.by_id"));
482 sortIDMenuItem.addActionListener(new ActionListener()
485 public void actionPerformed(ActionEvent e)
487 sortIDMenuItem_actionPerformed(e);
490 JMenuItem sortLengthMenuItem = new JMenuItem(
491 MessageManager.getString("action.by_length"));
492 sortLengthMenuItem.addActionListener(new ActionListener()
495 public void actionPerformed(ActionEvent e)
497 sortLengthMenuItem_actionPerformed(e);
500 JMenuItem sortGroupMenuItem = new JMenuItem(
501 MessageManager.getString("action.by_group"));
502 sortGroupMenuItem.addActionListener(new ActionListener()
505 public void actionPerformed(ActionEvent e)
507 sortGroupMenuItem_actionPerformed(e);
511 JMenuItem removeRedundancyMenuItem = new JMenuItem(
512 MessageManager.getString("action.remove_redundancy"));
513 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
514 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
515 al = new ActionListener()
518 public void actionPerformed(ActionEvent e)
520 removeRedundancyMenuItem_actionPerformed(e);
523 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
525 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
526 MessageManager.getString("action.pairwise_alignment"));
527 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
530 public void actionPerformed(ActionEvent e)
532 pairwiseAlignmentMenuItem_actionPerformed(e);
536 this.getContentPane().setLayout(new BorderLayout());
537 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
538 statusBar.setBackground(Color.white);
539 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
540 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
541 statusBar.setText(MessageManager.getString("label.status_bar"));
543 .setText(MessageManager.getString("label.out_to_textbox"));
545 annotationPanelMenuItem.setActionCommand("");
546 annotationPanelMenuItem
547 .setText(MessageManager.getString("label.show_annotations"));
548 annotationPanelMenuItem
549 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
550 annotationPanelMenuItem.addActionListener(new ActionListener()
553 public void actionPerformed(ActionEvent e)
555 annotationPanelMenuItem_actionPerformed(e);
558 showAllAlAnnotations.setText(
559 MessageManager.getString("label.show_all_al_annotations"));
560 final boolean isAnnotationPanelShown = annotationPanelMenuItem
562 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
563 showAllAlAnnotations.addActionListener(new ActionListener()
566 public void actionPerformed(ActionEvent e)
568 showAllAnnotations_actionPerformed(false, true);
571 hideAllAlAnnotations.setText(
572 MessageManager.getString("label.hide_all_al_annotations"));
573 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
574 hideAllAlAnnotations.addActionListener(new ActionListener()
577 public void actionPerformed(ActionEvent e)
579 hideAllAnnotations_actionPerformed(false, true);
582 showAllSeqAnnotations.setText(
583 MessageManager.getString("label.show_all_seq_annotations"));
584 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
585 showAllSeqAnnotations.addActionListener(new ActionListener()
588 public void actionPerformed(ActionEvent e)
590 showAllAnnotations_actionPerformed(true, false);
593 hideAllSeqAnnotations.setText(
594 MessageManager.getString("label.hide_all_seq_annotations"));
595 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
596 hideAllSeqAnnotations.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent e)
601 hideAllAnnotations_actionPerformed(true, false);
604 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
605 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
606 SequenceAnnotationOrder.NONE.name()));
607 sortAnnBySequence = new JCheckBoxMenuItem(
608 MessageManager.getString("label.sort_annotations_by_sequence"));
609 sortAnnByLabel = new JCheckBoxMenuItem(
610 MessageManager.getString("label.sort_annotations_by_label"));
612 sortAnnBySequence.addActionListener(new ActionListener()
615 public void actionPerformed(ActionEvent e)
617 setAnnotationSortOrder(SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
621 sortAnnByLabel.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent e)
626 setAnnotationSortOrder(SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
630 colourTextMenuItem = new JCheckBoxMenuItem(
631 MessageManager.getString("label.colour_text"));
632 colourTextMenuItem.addActionListener(new ActionListener()
635 public void actionPerformed(ActionEvent e)
637 colourTextMenuItem_actionPerformed(e);
641 JMenuItem htmlMenuItem = new JMenuItem(
642 MessageManager.getString("label.html"));
643 htmlMenuItem.addActionListener(new ActionListener()
646 public void actionPerformed(ActionEvent e)
648 htmlMenuItem_actionPerformed(e);
652 JMenuItem createBioJS = new JMenuItem(
653 MessageManager.getString("label.biojs_html_export"));
654 createBioJS.addActionListener(new java.awt.event.ActionListener()
657 public void actionPerformed(ActionEvent e)
659 bioJSMenuItem_actionPerformed(e);
663 JMenuItem overviewMenuItem = new JMenuItem(
664 MessageManager.getString("label.overview_window"));
665 overviewMenuItem.addActionListener(new ActionListener()
668 public void actionPerformed(ActionEvent e)
670 overviewMenuItem_actionPerformed(e);
674 undoMenuItem.setEnabled(false);
675 undoMenuItem.setText(MessageManager.getString("action.undo"));
676 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
677 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
678 al = new ActionListener()
681 public void actionPerformed(ActionEvent e)
683 undoMenuItem_actionPerformed(e);
686 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
688 redoMenuItem.setEnabled(false);
689 redoMenuItem.setText(MessageManager.getString("action.redo"));
690 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
691 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
692 al = new ActionListener()
695 public void actionPerformed(ActionEvent e)
697 redoMenuItem_actionPerformed(e);
700 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
702 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
703 wrapMenuItem.addActionListener(new ActionListener()
706 public void actionPerformed(ActionEvent e)
708 wrapMenuItem_actionPerformed(e);
712 JMenuItem printMenuItem = new JMenuItem(
713 MessageManager.getString("action.print"));
714 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
715 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
716 al = new ActionListener()
719 public void actionPerformed(ActionEvent e)
721 printMenuItem_actionPerformed(e);
724 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
727 .setText(MessageManager.getString("action.show_gaps"));
728 renderGapsMenuItem.setState(true);
729 renderGapsMenuItem.addActionListener(new ActionListener()
732 public void actionPerformed(ActionEvent e)
734 renderGapsMenuItem_actionPerformed(e);
738 JMenuItem findMenuItem = new JMenuItem(
739 MessageManager.getString("action.find"));
740 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
741 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
742 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
743 MessageManager.getString("label.find_tip")));
744 al = new ActionListener()
747 public void actionPerformed(ActionEvent e)
749 findMenuItem_actionPerformed(e);
752 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
754 showSeqFeatures.setText(
755 MessageManager.getString("label.show_sequence_features"));
756 showSeqFeatures.addActionListener(new ActionListener()
759 public void actionPerformed(ActionEvent actionEvent)
761 showSeqFeatures_actionPerformed(actionEvent);
765 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
766 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
767 * void actionPerformed(ActionEvent actionEvent) {
768 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
771 .setText(MessageManager.getString("label.show_database_refs"));
772 showDbRefsMenuitem.addActionListener(new ActionListener()
776 public void actionPerformed(ActionEvent e)
778 showDbRefs_actionPerformed(e);
782 showNpFeatsMenuitem.setText(
783 MessageManager.getString("label.show_non_positional_features"));
784 showNpFeatsMenuitem.addActionListener(new ActionListener()
788 public void actionPerformed(ActionEvent e)
790 showNpFeats_actionPerformed(e);
794 showGroupConservation
795 .setText(MessageManager.getString("label.group_conservation"));
796 showGroupConservation.addActionListener(new ActionListener()
800 public void actionPerformed(ActionEvent e)
802 showGroupConservation_actionPerformed(e);
808 .setText(MessageManager.getString("label.group_consensus"));
809 showGroupConsensus.addActionListener(new ActionListener()
813 public void actionPerformed(ActionEvent e)
815 showGroupConsensus_actionPerformed(e);
819 showConsensusHistogram.setText(
820 MessageManager.getString("label.show_consensus_histogram"));
821 showConsensusHistogram.addActionListener(new ActionListener()
825 public void actionPerformed(ActionEvent e)
827 showConsensusHistogram_actionPerformed(e);
832 .setText(MessageManager.getString("label.show_consensus_logo"));
833 showSequenceLogo.addActionListener(new ActionListener()
837 public void actionPerformed(ActionEvent e)
839 showSequenceLogo_actionPerformed(e);
843 normaliseSequenceLogo
844 .setText(MessageManager.getString("label.norm_consensus_logo"));
845 normaliseSequenceLogo.addActionListener(new ActionListener()
849 public void actionPerformed(ActionEvent e)
851 normaliseSequenceLogo_actionPerformed(e);
855 applyAutoAnnotationSettings
856 .setText(MessageManager.getString("label.apply_all_groups"));
857 applyAutoAnnotationSettings.setState(false);
858 applyAutoAnnotationSettings.setVisible(true);
859 applyAutoAnnotationSettings.addActionListener(new ActionListener()
862 public void actionPerformed(ActionEvent e)
864 applyAutoAnnotationSettings_actionPerformed(e);
868 ButtonGroup buttonGroup = new ButtonGroup();
869 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
870 MessageManager.getString("label.show_first"));
871 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
872 MessageManager.getString("label.show_last"));
873 buttonGroup.add(showAutoFirst);
874 buttonGroup.add(showAutoLast);
875 final boolean autoFirst = Cache
876 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
877 showAutoFirst.setSelected(autoFirst);
878 showAutoFirst.addActionListener(new ActionListener()
881 public void actionPerformed(ActionEvent e)
883 if (setShowAutoCalculatedAbove(showAutoFirst.isSelected()))
889 showAutoLast.setSelected(!showAutoFirst.isSelected());
890 showAutoLast.addActionListener(new ActionListener()
893 public void actionPerformed(ActionEvent e)
895 if (setShowAutoCalculatedAbove(!showAutoLast.isSelected()))
902 JMenuItem deleteGroups = new JMenuItem(
903 MessageManager.getString("action.undefine_groups"));
904 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
905 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
906 al = new ActionListener()
909 public void actionPerformed(ActionEvent e)
911 deleteGroups_actionPerformed(e);
914 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
916 JMenuItem annotationColumn = new JMenuItem(
917 MessageManager.getString("action.select_by_annotation"));
918 annotationColumn.addActionListener(new ActionListener()
921 public void actionPerformed(ActionEvent e)
923 annotationColumn_actionPerformed(e);
927 JMenuItem createGroup = new JMenuItem(
928 MessageManager.getString("action.create_group"));
929 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
930 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
931 al = new ActionListener()
934 public void actionPerformed(ActionEvent e)
936 createGroup_actionPerformed(e);
939 addMenuActionAndAccelerator(keyStroke, createGroup, al);
941 JMenuItem unGroup = new JMenuItem(
942 MessageManager.getString("action.remove_group"));
943 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
944 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
945 | KeyEvent.SHIFT_MASK,
947 al = new ActionListener()
950 public void actionPerformed(ActionEvent e)
952 unGroup_actionPerformed(e);
955 addMenuActionAndAccelerator(keyStroke, unGroup, al);
957 copy.setText(MessageManager.getString("action.copy"));
958 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
959 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
961 al = new ActionListener()
964 public void actionPerformed(ActionEvent e)
966 copy_actionPerformed(e);
969 addMenuActionAndAccelerator(keyStroke, copy, al);
971 cut.setText(MessageManager.getString("action.cut"));
972 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
973 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
974 al = new ActionListener()
977 public void actionPerformed(ActionEvent e)
979 cut_actionPerformed(e);
982 addMenuActionAndAccelerator(keyStroke, cut, al);
984 JMenuItem delete = new JMenuItem(
985 MessageManager.getString("action.delete"));
986 delete.addActionListener(new ActionListener()
989 public void actionPerformed(ActionEvent e)
991 delete_actionPerformed(e);
995 pasteMenu.setText(MessageManager.getString("action.paste"));
996 JMenuItem pasteNew = new JMenuItem(
997 MessageManager.getString("label.to_new_alignment"));
998 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
999 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1000 | KeyEvent.SHIFT_MASK,
1002 al = new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 pasteNew_actionPerformed(e);
1010 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1012 JMenuItem pasteThis = new JMenuItem(
1013 MessageManager.getString("label.to_this_alignment"));
1014 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1015 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1016 al = new ActionListener()
1019 public void actionPerformed(ActionEvent e)
1021 pasteThis_actionPerformed(e);
1024 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1026 JMenuItem createPNG = new JMenuItem("PNG");
1027 createPNG.addActionListener(new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1035 createPNG.setActionCommand(
1036 MessageManager.getString("label.save_png_image"));
1038 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1039 font.addActionListener(new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 font_actionPerformed(e);
1048 MessageManager.getString("label.show_sequence_limits"));
1049 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1050 seqLimits.addActionListener(new ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 seqLimit_actionPerformed(e);
1058 JMenuItem epsFile = new JMenuItem("EPS");
1059 epsFile.addActionListener(new ActionListener()
1062 public void actionPerformed(ActionEvent e)
1068 JMenuItem createSVG = new JMenuItem("SVG");
1069 createSVG.addActionListener(new ActionListener()
1072 public void actionPerformed(ActionEvent e)
1078 JMenuItem loadTreeMenuItem = new JMenuItem(
1079 MessageManager.getString("label.load_associated_tree"));
1080 loadTreeMenuItem.setActionCommand(
1081 MessageManager.getString("label.load_tree_for_sequence_set"));
1082 loadTreeMenuItem.addActionListener(new ActionListener()
1085 public void actionPerformed(ActionEvent e)
1087 loadTreeMenuItem_actionPerformed(e);
1091 scaleAbove.setVisible(false);
1092 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1093 scaleAbove.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent e)
1098 scaleAbove_actionPerformed(e);
1101 scaleLeft.setVisible(false);
1102 scaleLeft.setSelected(true);
1103 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1104 scaleLeft.addActionListener(new ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 scaleLeft_actionPerformed(e);
1112 scaleRight.setVisible(false);
1113 scaleRight.setSelected(true);
1114 scaleRight.setText(MessageManager.getString("action.scale_right"));
1115 scaleRight.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 scaleRight_actionPerformed(e);
1123 centreColumnLabelsMenuItem.setVisible(true);
1124 centreColumnLabelsMenuItem.setState(false);
1125 centreColumnLabelsMenuItem.setText(
1126 MessageManager.getString("label.centre_column_labels"));
1127 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 centreColumnLabels_actionPerformed(e);
1135 followHighlightMenuItem.setVisible(true);
1136 followHighlightMenuItem.setState(true);
1137 followHighlightMenuItem
1138 .setText(MessageManager.getString("label.automatic_scrolling"));
1139 followHighlightMenuItem.addActionListener(new ActionListener()
1143 public void actionPerformed(ActionEvent e)
1145 followHighlight_actionPerformed();
1151 .setText(MessageManager.getString("action.by_tree_order"));
1152 sort.setText(MessageManager.getString("action.sort"));
1153 sort.addMenuListener(new MenuListener()
1156 public void menuSelected(MenuEvent e)
1158 buildTreeSortMenu();
1162 public void menuDeselected(MenuEvent e)
1167 public void menuCanceled(MenuEvent e)
1172 .setText(MessageManager.getString("label.sort_by_score"));
1173 sort.add(sortByAnnotScore);
1174 sort.addMenuListener(new javax.swing.event.MenuListener()
1178 public void menuCanceled(MenuEvent e)
1183 public void menuDeselected(MenuEvent e)
1188 public void menuSelected(MenuEvent e)
1190 buildSortByAnnotationScoresMenu();
1193 sortByAnnotScore.setVisible(false);
1196 .setText(MessageManager.getString("action.calculate_tree_pca"));
1198 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1200 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1201 padGapsMenuitem.addActionListener(new ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 padGapsMenuitem_actionPerformed(e);
1209 JMenuItem vamsasStore = new JMenuItem(
1210 MessageManager.getString("label.vamsas_store"));
1211 vamsasStore.setVisible(false);
1212 vamsasStore.addActionListener(new ActionListener()
1215 public void actionPerformed(ActionEvent e)
1217 vamsasStore_actionPerformed(e);
1222 * Translate as cDNA with sub-menu of translation tables
1224 showTranslation.setText(MessageManager
1225 .getString("label.translate_cDNA"));
1226 boolean first = true;
1227 for (final GeneticCodeI table : GeneticCodes.getInstance()
1230 JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
1231 showTranslation.add(item);
1232 item.addActionListener(new ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 showTranslation_actionPerformed(table);
1242 showTranslation.addSeparator();
1247 showReverse.setText(MessageManager.getString("label.reverse"));
1248 showReverse.addActionListener(new ActionListener()
1251 public void actionPerformed(ActionEvent e)
1253 showReverse_actionPerformed(false);
1256 showReverseComplement
1257 .setText(MessageManager.getString("label.reverse_complement"));
1258 showReverseComplement.addActionListener(new ActionListener()
1261 public void actionPerformed(ActionEvent e)
1263 showReverse_actionPerformed(true);
1267 JMenuItem extractScores = new JMenuItem(
1268 MessageManager.getString("label.extract_scores"));
1269 extractScores.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 extractScores_actionPerformed(e);
1277 extractScores.setVisible(true);
1278 // JBPNote: TODO: make gui for regex based score extraction
1280 // for show products actions see AlignFrame.canShowProducts
1281 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1283 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1284 runGroovy.setToolTipText(
1285 MessageManager.getString("label.run_groovy_tip"));
1286 runGroovy.addActionListener(new ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 runGroovy_actionPerformed();
1295 JMenuItem openFeatureSettings = new JMenuItem(
1296 MessageManager.getString("action.feature_settings"));
1297 openFeatureSettings.addActionListener(new ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 featureSettings_actionPerformed(e);
1305 JMenuItem fetchSequence = new JMenuItem(
1306 MessageManager.getString("label.fetch_sequences"));
1307 fetchSequence.addActionListener(new ActionListener()
1310 public void actionPerformed(ActionEvent e)
1312 fetchSequence_actionPerformed(e);
1316 JMenuItem associatedData = new JMenuItem(
1317 MessageManager.getString("label.load_features_annotations"));
1318 associatedData.addActionListener(new ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 associatedData_actionPerformed(e);
1326 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1327 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1328 loadVcf.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 loadVcf_actionPerformed();
1336 autoCalculate.setText(
1337 MessageManager.getString("label.autocalculate_consensus"));
1338 autoCalculate.setState(
1339 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1340 autoCalculate.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 autoCalculate_actionPerformed(e);
1349 MessageManager.getString("label.sort_alignment_new_tree"));
1350 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1351 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1353 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1354 sortByTree.addActionListener(new ActionListener()
1357 public void actionPerformed(ActionEvent e)
1359 sortByTreeOption_actionPerformed(e);
1363 listenToViewSelections.setText(
1364 MessageManager.getString("label.listen_for_selections"));
1365 listenToViewSelections
1366 .setToolTipText("<html>" + MessageManager.getString(
1367 "label.selections_mirror_selections_made_same_sequences_other_views"));
1368 listenToViewSelections.setState(false);
1369 listenToViewSelections.addActionListener(new ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 listenToViewSelections_actionPerformed(e);
1378 JMenu addSequenceMenu = new JMenu(
1379 MessageManager.getString("label.add_sequences"));
1380 JMenuItem addFromFile = new JMenuItem(
1381 MessageManager.getString("label.from_file"));
1382 addFromFile.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 addFromFile_actionPerformed(e);
1390 JMenuItem addFromText = new JMenuItem(
1391 MessageManager.getString("label.from_textbox"));
1392 addFromText.addActionListener(new ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 addFromText_actionPerformed(e);
1400 JMenuItem addFromURL = new JMenuItem(
1401 MessageManager.getString("label.from_url"));
1402 addFromURL.addActionListener(new ActionListener()
1405 public void actionPerformed(ActionEvent e)
1407 addFromURL_actionPerformed(e);
1410 JMenuItem exportFeatures = new JMenuItem(
1411 MessageManager.getString("label.export_features"));
1412 exportFeatures.addActionListener(new ActionListener()
1415 public void actionPerformed(ActionEvent e)
1417 exportFeatures_actionPerformed(e);
1420 JMenuItem exportAnnotations = new JMenuItem(
1421 MessageManager.getString("label.export_annotations"));
1422 exportAnnotations.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 exportAnnotations_actionPerformed(e);
1430 statusPanel.setLayout(new GridLayout());
1431 JMenuItem showAllSeqs = new JMenuItem(
1432 MessageManager.getString("label.all_sequences"));
1433 showAllSeqs.setToolTipText(
1434 MessageManager.getString("label.toggle_sequence_visibility"));
1435 showAllSeqs.addActionListener(new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1440 showAllSeqs_actionPerformed(e);
1443 JMenuItem showAllColumns = new JMenuItem(
1444 MessageManager.getString("label.all_columns"));
1445 showAllColumns.setToolTipText(
1446 MessageManager.getString("label.toggle_columns_visibility"));
1447 showAllColumns.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 showAllColumns_actionPerformed(e);
1455 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1456 JMenuItem hideSelSequences = new JMenuItem(
1457 MessageManager.getString("label.selected_sequences"));
1458 hideSelSequences.setToolTipText(
1459 MessageManager.getString("label.toggle_sequence_visibility"));
1460 hideSelSequences.addActionListener(new ActionListener()
1463 public void actionPerformed(ActionEvent e)
1465 hideSelSequences_actionPerformed(e);
1468 JMenuItem hideSelColumns = new JMenuItem(
1469 MessageManager.getString("label.selected_columns"));
1470 hideSelColumns.setToolTipText(
1471 MessageManager.getString("label.toggle_columns_visibility"));
1472 hideSelColumns.addActionListener(new ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 hideSelColumns_actionPerformed(e);
1480 JMenuItem hideAllSelection = new JMenuItem(
1481 MessageManager.getString("label.selected_region"));
1482 hideAllSelection.addActionListener(new ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 hideAllSelection_actionPerformed(e);
1490 // TODO: should be hidden if no selection exists.
1491 JMenuItem hideAllButSelection = new JMenuItem(
1492 MessageManager.getString("label.all_but_selected_region"));
1493 hideAllButSelection.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 hideAllButSelection_actionPerformed(e);
1501 JMenuItem showAllhidden = new JMenuItem(
1502 MessageManager.getString("label.all_sequences_columns"));
1503 showAllhidden.setToolTipText(MessageManager
1504 .getString("label.toggles_visibility_hidden_selected_regions"));
1505 showAllhidden.addActionListener(new ActionListener()
1508 public void actionPerformed(ActionEvent e)
1510 showAllhidden_actionPerformed(e);
1513 hiddenMarkers.setText(
1514 MessageManager.getString("action.show_hidden_markers"));
1515 hiddenMarkers.addActionListener(new ActionListener()
1518 public void actionPerformed(ActionEvent e)
1520 hiddenMarkers_actionPerformed(e);
1524 JMenuItem invertColSel = new JMenuItem(
1525 MessageManager.getString("action.invert_column_selection"));
1526 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1527 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1528 | KeyEvent.ALT_MASK,
1530 al = new ActionListener()
1533 public void actionPerformed(ActionEvent e)
1535 invertColSel_actionPerformed(e);
1538 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1540 showComplementMenuItem.setVisible(false);
1541 showComplementMenuItem.addActionListener(new ActionListener()
1544 public void actionPerformed(ActionEvent e)
1546 showComplement_actionPerformed(showComplementMenuItem.getState());
1550 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1553 public void stateChanged(ChangeEvent evt)
1555 JTabbedPane pane = (JTabbedPane) evt.getSource();
1556 int sel = pane.getSelectedIndex();
1557 tabSelectionChanged(sel);
1560 tabbedPane.addMouseListener(new MouseAdapter()
1563 public void mousePressed(MouseEvent e)
1565 if (e.isPopupTrigger()) // Mac
1567 tabbedPane_mousePressed(e);
1572 public void mouseReleased(MouseEvent e)
1574 if (e.isPopupTrigger()) // Windows
1576 tabbedPane_mousePressed(e);
1580 tabbedPane.addFocusListener(new FocusAdapter()
1583 public void focusGained(FocusEvent e)
1585 tabbedPane_focusGained(e);
1589 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1590 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1591 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1592 al = new ActionListener()
1595 public void actionPerformed(ActionEvent e)
1597 save_actionPerformed(e);
1600 addMenuActionAndAccelerator(keyStroke, save, al);
1602 reload.setEnabled(false);
1603 reload.setText(MessageManager.getString("action.reload"));
1604 reload.addActionListener(new ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 reload_actionPerformed(e);
1613 JMenuItem newView = new JMenuItem(
1614 MessageManager.getString("action.new_view"));
1615 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1616 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1617 al = new ActionListener()
1620 public void actionPerformed(ActionEvent e)
1622 newView_actionPerformed(e);
1625 addMenuActionAndAccelerator(keyStroke, newView, al);
1627 tabbedPane.setToolTipText("<html><i>"
1628 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1631 formatMenu.setText(MessageManager.getString("action.format"));
1632 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1634 idRightAlign.setText(
1635 MessageManager.getString("label.right_align_sequence_id"));
1636 idRightAlign.addActionListener(new ActionListener()
1639 public void actionPerformed(ActionEvent e)
1641 idRightAlign_actionPerformed(e);
1645 gatherViews.setEnabled(false);
1646 gatherViews.setText(MessageManager.getString("action.gather_views"));
1647 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1648 al = new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 gatherViews_actionPerformed(e);
1656 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1658 expandViews.setEnabled(false);
1659 expandViews.setText(MessageManager.getString("action.expand_views"));
1660 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1661 al = new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 expandViews_actionPerformed(e);
1669 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1671 JMenuItem pageSetup = new JMenuItem(
1672 MessageManager.getString("action.page_setup"));
1673 pageSetup.addActionListener(new ActionListener()
1676 public void actionPerformed(ActionEvent e)
1678 pageSetup_actionPerformed(e);
1681 JMenuItem alignmentProperties = new JMenuItem(
1682 MessageManager.getString("label.alignment_props"));
1683 alignmentProperties.addActionListener(new ActionListener()
1686 public void actionPerformed(ActionEvent actionEvent)
1688 alignmentProperties();
1691 JMenuItem selectHighlighted = new JMenuItem(
1692 MessageManager.getString("action.select_highlighted_columns"));
1693 selectHighlighted.setToolTipText(
1694 MessageManager.getString("tooltip.select_highlighted_columns"));
1695 al = new ActionListener()
1698 public void actionPerformed(ActionEvent actionEvent)
1700 selectHighlightedColumns_actionPerformed(actionEvent);
1703 selectHighlighted.addActionListener(al);
1704 JMenu tooltipSettingsMenu = new JMenu(
1705 MessageManager.getString("label.sequence_id_tooltip"));
1706 JMenu autoAnnMenu = new JMenu(
1707 MessageManager.getString("label.autocalculated_annotation"));
1709 JMenu exportImageMenu = new JMenu(
1710 MessageManager.getString("label.export_image"));
1711 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1712 alignFrameMenuBar.add(fileMenu);
1713 alignFrameMenuBar.add(editMenu);
1714 alignFrameMenuBar.add(selectMenu);
1715 alignFrameMenuBar.add(viewMenu);
1716 alignFrameMenuBar.add(annotationsMenu);
1717 alignFrameMenuBar.add(formatMenu);
1718 alignFrameMenuBar.add(colourMenu);
1719 alignFrameMenuBar.add(calculateMenu);
1720 alignFrameMenuBar.add(webService);
1722 fileMenu.add(fetchSequence);
1723 fileMenu.add(addSequenceMenu);
1724 fileMenu.add(reload);
1725 fileMenu.addSeparator();
1726 fileMenu.add(vamsasStore);
1728 fileMenu.add(saveAs);
1729 fileMenu.add(outputTextboxMenu);
1730 fileMenu.add(pageSetup);
1731 fileMenu.add(printMenuItem);
1732 fileMenu.addSeparator();
1733 fileMenu.add(exportImageMenu);
1734 fileMenu.add(exportFeatures);
1735 fileMenu.add(exportAnnotations);
1736 fileMenu.add(loadTreeMenuItem);
1737 fileMenu.add(associatedData);
1738 fileMenu.add(loadVcf);
1739 fileMenu.addSeparator();
1740 fileMenu.add(closeMenuItem);
1742 pasteMenu.add(pasteNew);
1743 pasteMenu.add(pasteThis);
1744 editMenu.add(undoMenuItem);
1745 editMenu.add(redoMenuItem);
1748 editMenu.add(pasteMenu);
1749 editMenu.add(delete);
1750 editMenu.addSeparator();
1751 editMenu.add(remove2LeftMenuItem);
1752 editMenu.add(remove2RightMenuItem);
1753 editMenu.add(removeGappedColumnMenuItem);
1754 editMenu.add(removeAllGapsMenuItem);
1755 editMenu.add(removeRedundancyMenuItem);
1756 editMenu.addSeparator();
1757 // dont add these yet in the CVS build - they cannot be undone!
1758 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1759 // editMenu.add(justifyLeftMenuItem);
1760 // editMenu.add(justifyRightMenuItem);
1761 // editMenu.addSeparator();
1762 editMenu.add(padGapsMenuitem);
1764 showMenu.add(showAllColumns);
1765 showMenu.add(showAllSeqs);
1766 showMenu.add(showAllhidden);
1767 hideMenu.add(hideSelColumns);
1768 hideMenu.add(hideSelSequences);
1769 hideMenu.add(hideAllSelection);
1770 hideMenu.add(hideAllButSelection);
1771 viewMenu.add(newView);
1772 viewMenu.add(expandViews);
1773 viewMenu.add(gatherViews);
1774 viewMenu.addSeparator();
1775 viewMenu.add(showMenu);
1776 viewMenu.add(hideMenu);
1777 viewMenu.add(showComplementMenuItem);
1778 viewMenu.addSeparator();
1779 viewMenu.add(followHighlightMenuItem);
1780 viewMenu.addSeparator();
1781 viewMenu.add(showSeqFeatures);
1782 // viewMenu.add(showSeqFeaturesHeight);
1783 viewMenu.add(openFeatureSettings);
1784 tooltipSettingsMenu.add(showDbRefsMenuitem);
1785 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1786 viewMenu.add(tooltipSettingsMenu);
1787 viewMenu.addSeparator();
1788 viewMenu.add(alignmentProperties);
1789 viewMenu.addSeparator();
1790 viewMenu.add(overviewMenuItem);
1792 annotationsMenu.add(annotationPanelMenuItem);
1793 annotationsMenu.addSeparator();
1794 annotationsMenu.add(showAllAlAnnotations);
1795 annotationsMenu.add(hideAllAlAnnotations);
1796 annotationsMenu.addSeparator();
1797 annotationsMenu.add(showAllSeqAnnotations);
1798 annotationsMenu.add(hideAllSeqAnnotations);
1799 annotationsMenu.add(sortAnnBySequence);
1800 annotationsMenu.add(sortAnnByLabel);
1801 annotationsMenu.addSeparator();
1802 autoAnnMenu.add(showAutoFirst);
1803 autoAnnMenu.add(showAutoLast);
1804 autoAnnMenu.addSeparator();
1805 autoAnnMenu.add(applyAutoAnnotationSettings);
1806 autoAnnMenu.add(showConsensusHistogram);
1807 autoAnnMenu.add(showSequenceLogo);
1808 autoAnnMenu.add(normaliseSequenceLogo);
1809 autoAnnMenu.addSeparator();
1810 autoAnnMenu.add(showGroupConservation);
1811 autoAnnMenu.add(showGroupConsensus);
1812 annotationsMenu.add(autoAnnMenu);
1814 sort.add(sortIDMenuItem);
1815 sort.add(sortLengthMenuItem);
1816 sort.add(sortGroupMenuItem);
1817 sort.add(sortPairwiseMenuItem);
1818 sort.add(sortByTreeMenu);
1819 calculateMenu.add(sort);
1820 calculateMenu.add(calculateTree);
1821 calculateMenu.addSeparator();
1822 calculateMenu.add(pairwiseAlignmentMenuItem);
1823 calculateMenu.addSeparator();
1824 calculateMenu.add(showTranslation);
1825 calculateMenu.add(showReverse);
1826 calculateMenu.add(showReverseComplement);
1827 calculateMenu.add(showProducts);
1828 calculateMenu.add(autoCalculate);
1829 calculateMenu.add(sortByTree);
1830 calculateMenu.addSeparator();
1831 calculateMenu.add(expandAlignment);
1832 calculateMenu.add(extractScores);
1833 calculateMenu.addSeparator();
1834 calculateMenu.add(runGroovy);
1836 webServiceNoServices = new JMenuItem(
1837 MessageManager.getString("label.no_services"));
1838 webService.add(webServiceNoServices);
1839 exportImageMenu.add(htmlMenuItem);
1840 exportImageMenu.add(epsFile);
1841 exportImageMenu.add(createPNG);
1842 exportImageMenu.add(createBioJS);
1843 exportImageMenu.add(createSVG);
1844 addSequenceMenu.add(addFromFile);
1845 addSequenceMenu.add(addFromText);
1846 addSequenceMenu.add(addFromURL);
1847 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1848 statusPanel.add(statusBar, null);
1849 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1851 formatMenu.add(font);
1852 formatMenu.addSeparator();
1853 formatMenu.add(wrapMenuItem);
1854 formatMenu.add(scaleAbove);
1855 formatMenu.add(scaleLeft);
1856 formatMenu.add(scaleRight);
1857 formatMenu.add(seqLimits);
1858 formatMenu.add(idRightAlign);
1859 formatMenu.add(hiddenMarkers);
1860 formatMenu.add(viewBoxesMenuItem);
1861 formatMenu.add(viewTextMenuItem);
1862 formatMenu.add(colourTextMenuItem);
1863 formatMenu.add(renderGapsMenuItem);
1864 formatMenu.add(centreColumnLabelsMenuItem);
1865 formatMenu.add(showNonconservedMenuItem);
1866 selectMenu.add(findMenuItem);
1867 selectMenu.addSeparator();
1868 selectMenu.add(selectAllSequenceMenuItem);
1869 selectMenu.add(deselectAllSequenceMenuItem);
1870 selectMenu.add(invertSequenceMenuItem);
1871 selectMenu.add(invertColSel);
1872 selectMenu.add(createGroup);
1873 selectMenu.add(unGroup);
1874 selectMenu.add(grpsFromSelection);
1875 selectMenu.add(deleteGroups);
1876 selectMenu.add(annotationColumn);
1877 selectMenu.add(selectHighlighted);
1878 // TODO - determine if the listenToViewSelections button is needed : see bug
1880 // selectMenu.addSeparator();
1881 // selectMenu.add(listenToViewSelections);
1884 protected void loadVcf_actionPerformed()
1889 * Constructs the entries on the Colour menu (but does not add them to the
1892 protected void initColourMenu()
1894 applyToAllGroups = new JCheckBoxMenuItem(
1895 MessageManager.getString("label.apply_colour_to_all_groups"));
1896 applyToAllGroups.addActionListener(new ActionListener()
1899 public void actionPerformed(ActionEvent e)
1901 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1905 textColour = new JMenuItem(
1906 MessageManager.getString("label.text_colour"));
1907 textColour.addActionListener(new ActionListener()
1910 public void actionPerformed(ActionEvent e)
1912 textColour_actionPerformed();
1916 conservationMenuItem = new JCheckBoxMenuItem(
1917 MessageManager.getString("action.by_conservation"));
1918 conservationMenuItem.addActionListener(new ActionListener()
1921 public void actionPerformed(ActionEvent e)
1923 conservationMenuItem_actionPerformed(
1924 conservationMenuItem.isSelected());
1928 abovePIDThreshold = new JCheckBoxMenuItem(
1929 MessageManager.getString("label.above_identity_threshold"));
1930 abovePIDThreshold.addActionListener(new ActionListener()
1933 public void actionPerformed(ActionEvent e)
1935 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1938 modifyPID = new JMenuItem(
1939 MessageManager.getString("label.modify_identity_threshold"));
1940 modifyPID.addActionListener(new ActionListener()
1943 public void actionPerformed(ActionEvent e)
1945 modifyPID_actionPerformed();
1948 modifyConservation = new JMenuItem(MessageManager
1949 .getString("label.modify_conservation_threshold"));
1950 modifyConservation.addActionListener(new ActionListener()
1953 public void actionPerformed(ActionEvent e)
1955 modifyConservation_actionPerformed();
1959 annotationColour = new JRadioButtonMenuItem(
1960 MessageManager.getString("action.by_annotation"));
1961 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1962 annotationColour.addActionListener(new ActionListener()
1965 public void actionPerformed(ActionEvent e)
1967 annotationColour_actionPerformed();
1972 protected void selectHighlightedColumns_actionPerformed(
1973 ActionEvent actionEvent)
1975 // TODO Auto-generated method stub
1980 * Generate the reverse sequence (or reverse complement if the flag is true)
1981 * and add it to the alignment
1985 protected void showReverse_actionPerformed(boolean complement)
1990 * Try to run script in a Groovy console, having first ensured that this
1991 * alignframe is set as currentAlignFrame in Desktop
1993 protected void runGroovy_actionPerformed()
1999 * Adds the given action listener and key accelerator to the given menu item.
2000 * Also saves in a lookup table to support lookup of action by key stroke.
2004 * @param actionListener
2006 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2007 JMenuItem menuItem, ActionListener actionListener)
2009 menuItem.setAccelerator(keyStroke);
2010 accelerators.put(keyStroke, menuItem);
2011 menuItem.addActionListener(actionListener);
2015 * Action on clicking sort annotations by type.
2019 protected void sortAnnotations()
2024 * Action on clicking Show all annotations.
2026 * @param forSequences
2027 * update sequence-related annotations
2028 * @param forAlignment
2029 * update non-sequence-related annotations
2031 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2032 boolean forAlignment)
2034 setAnnotationsVisibility(true, forSequences, forAlignment);
2038 * Action on clicking Hide all annotations.
2040 * @param forSequences
2041 * update sequence-related annotations
2042 * @param forAlignment
2043 * update non-sequence-related annotations
2045 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2046 boolean forAlignment)
2048 setAnnotationsVisibility(false, forSequences, forAlignment);
2052 * Set the visibility of annotations to true or false. Can act on
2053 * sequence-related annotations, or alignment-related, or both.
2056 * @param forSequences
2057 * update sequence-related annotations
2058 * @param forAlignment
2059 * update non-sequence-related annotations
2061 protected void setAnnotationsVisibility(boolean visible,
2062 boolean forSequences, boolean forAlignment)
2067 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2069 // TODO Auto-generated method stub
2073 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2075 // TODO Auto-generated method stub
2079 protected void showAllhidden_actionPerformed(ActionEvent e)
2081 // TODO Auto-generated method stub
2085 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2087 // TODO Auto-generated method stub
2091 protected void hideAllSelection_actionPerformed(ActionEvent e)
2093 // TODO Auto-generated method stub
2097 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2099 // TODO Auto-generated method stub
2103 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2105 // TODO Auto-generated method stub
2109 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2111 // TODO Auto-generated method stub
2115 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2117 // TODO Auto-generated method stub
2121 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2123 // TODO Auto-generated method stub
2127 protected void showGroupConservation_actionPerformed(ActionEvent e)
2129 // TODO Auto-generated method stub
2133 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2135 // TODO Auto-generated method stub
2139 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2141 // TODO Auto-generated method stub
2145 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2147 // TODO Auto-generated method stub
2151 protected void followHighlight_actionPerformed()
2153 // TODO Auto-generated method stub
2157 protected void showNpFeats_actionPerformed(ActionEvent e)
2159 // TODO Auto-generated method stub
2163 protected void showDbRefs_actionPerformed(ActionEvent e)
2165 // TODO Auto-generated method stub
2169 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2173 protected void buildSortByAnnotationScoresMenu()
2177 protected void extractScores_actionPerformed(ActionEvent e)
2181 protected void outputText_actionPerformed(ActionEvent e)
2185 public void addFromFile_actionPerformed(ActionEvent e)
2190 public void addFromText_actionPerformed(ActionEvent e)
2195 public void addFromURL_actionPerformed(ActionEvent e)
2200 public void exportFeatures_actionPerformed(ActionEvent e)
2205 public void exportAnnotations_actionPerformed(ActionEvent e)
2210 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2214 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2219 protected void closeMenuItem_actionPerformed(boolean b)
2223 protected void redoMenuItem_actionPerformed(ActionEvent e)
2227 protected void undoMenuItem_actionPerformed(ActionEvent e)
2231 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2235 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2239 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2243 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2247 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2251 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2255 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2259 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2263 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2267 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2271 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2275 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2279 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2283 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2287 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2291 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2295 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2299 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2303 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2307 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2311 protected void conservationMenuItem_actionPerformed(boolean selected)
2315 protected void printMenuItem_actionPerformed(ActionEvent e)
2319 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2323 protected void findMenuItem_actionPerformed(ActionEvent e)
2327 protected void abovePIDThreshold_actionPerformed(boolean selected)
2331 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2335 protected void deleteGroups_actionPerformed(ActionEvent e)
2339 protected void createGroup_actionPerformed(ActionEvent e)
2343 protected void unGroup_actionPerformed(ActionEvent e)
2347 protected void copy_actionPerformed(ActionEvent e)
2351 protected void cut_actionPerformed(ActionEvent e)
2355 protected void delete_actionPerformed(ActionEvent e)
2359 protected void pasteNew_actionPerformed(ActionEvent e)
2363 protected void pasteThis_actionPerformed(ActionEvent e)
2367 protected void applyToAllGroups_actionPerformed(boolean selected)
2371 public void createPNG(java.io.File f)
2375 protected void font_actionPerformed(ActionEvent e)
2379 protected void seqLimit_actionPerformed(ActionEvent e)
2383 public void seqDBRef_actionPerformed(ActionEvent e)
2388 public void createEPS(java.io.File f)
2392 public void createSVG(java.io.File f)
2397 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2403 * Template method to handle the 'load T-Coffee scores' menu event.
2405 * Subclasses override this method to provide a custom action.
2410 protected void loadScores_actionPerformed(ActionEvent event)
2415 protected void jpred_actionPerformed(ActionEvent e)
2419 protected void scaleAbove_actionPerformed(ActionEvent e)
2423 protected void scaleLeft_actionPerformed(ActionEvent e)
2427 protected void scaleRight_actionPerformed(ActionEvent e)
2431 protected void modifyPID_actionPerformed()
2435 protected void modifyConservation_actionPerformed()
2439 protected void saveAs_actionPerformed(ActionEvent e)
2443 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2447 public void vamsasStore_actionPerformed(ActionEvent e)
2452 public void vamsasLoad_actionPerformed(ActionEvent e)
2457 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
2462 public void featureSettings_actionPerformed(ActionEvent e)
2467 public void fetchSequence_actionPerformed(ActionEvent e)
2472 public void smoothFont_actionPerformed(ActionEvent e)
2477 public void annotationColour_actionPerformed()
2481 public void annotationColumn_actionPerformed(ActionEvent e)
2485 public void associatedData_actionPerformed(ActionEvent e)
2490 public void autoCalculate_actionPerformed(ActionEvent e)
2495 public void sortByTreeOption_actionPerformed(ActionEvent e)
2500 public void showAllSeqs_actionPerformed(ActionEvent e)
2505 public void showAllColumns_actionPerformed(ActionEvent e)
2510 public void hideSelSequences_actionPerformed(ActionEvent e)
2515 public void hideSelColumns_actionPerformed(ActionEvent e)
2520 public void hiddenMarkers_actionPerformed(ActionEvent e)
2525 public void findPdbId_actionPerformed(ActionEvent e)
2530 public void enterPdbId_actionPerformed(ActionEvent e)
2535 public void pdbFile_actionPerformed(ActionEvent e)
2540 public void invertColSel_actionPerformed(ActionEvent e)
2545 public void tabSelectionChanged(int sel)
2550 public void tabbedPane_mousePressed(MouseEvent e)
2555 public void tabbedPane_focusGained(FocusEvent e)
2560 public void save_actionPerformed(ActionEvent e)
2565 public void reload_actionPerformed(ActionEvent e)
2570 public void newView_actionPerformed(ActionEvent e)
2575 public void textColour_actionPerformed()
2580 public void idRightAlign_actionPerformed(ActionEvent e)
2585 public void expandViews_actionPerformed(ActionEvent e)
2590 public void gatherViews_actionPerformed(ActionEvent e)
2595 public void buildTreeSortMenu()
2600 public void pageSetup_actionPerformed(ActionEvent e)
2605 public void alignmentProperties()
2610 protected void expand_newalign(ActionEvent e)
2612 // TODO Auto-generated method stub
2617 * Sets the value of the flag for 'show autocalculated annotations above other
2618 * annotations'. Answers true if the value changed, else false.
2620 * @param showAutoCalculatedAbove
2623 protected boolean setShowAutoCalculatedAbove(
2624 boolean showAutoCalculatedAbove)
2629 public void setAnnotationSortOrder(
2630 SequenceAnnotationOrder annotationSortOrder)
2634 public Map<KeyStroke, JMenuItem> getAccelerators()
2636 return this.accelerators;
2640 * Returns the selected index of the tabbed pane, or -1 if none selected
2641 * (including the case where the tabbed pane has not been made visible).
2645 public int getTabIndex()
2647 return tabbedPane.getSelectedIndex();
2650 public JPanel getStatusPanel()
2656 * Sets a reference to the containing split frame. Also makes the 'toggle
2657 * split view' menu item visible and checked.
2661 public void setSplitFrame(SplitContainerI sf)
2663 this.splitFrame = sf;
2666 this.showComplementMenuItem.setVisible(true);
2667 this.showComplementMenuItem.setState(true);
2671 public SplitContainerI getSplitViewContainer()
2673 return this.splitFrame;
2676 protected void showComplement_actionPerformed(boolean complement)