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.api.SplitContainerI;
25 import jalview.bin.Cache;
26 import jalview.gui.JvSwingUtils;
27 import jalview.gui.Preferences;
28 import jalview.io.FileFormats;
29 import jalview.util.MessageManager;
30 import jalview.util.Platform;
32 import java.awt.BorderLayout;
33 import java.awt.Color;
34 import java.awt.GridLayout;
35 import java.awt.Toolkit;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.FocusAdapter;
39 import java.awt.event.FocusEvent;
40 import java.awt.event.KeyEvent;
41 import java.awt.event.MouseAdapter;
42 import java.awt.event.MouseEvent;
43 import java.util.HashMap;
46 import javax.swing.BorderFactory;
47 import javax.swing.ButtonGroup;
48 import javax.swing.JCheckBoxMenuItem;
49 import javax.swing.JInternalFrame;
50 import javax.swing.JLabel;
51 import javax.swing.JMenu;
52 import javax.swing.JMenuBar;
53 import javax.swing.JMenuItem;
54 import javax.swing.JPanel;
55 import javax.swing.JRadioButtonMenuItem;
56 import javax.swing.JTabbedPane;
57 import javax.swing.KeyStroke;
58 import javax.swing.event.ChangeEvent;
59 import javax.swing.event.MenuEvent;
60 import javax.swing.event.MenuListener;
62 public class GAlignFrame extends JInternalFrame
64 protected JMenuBar alignFrameMenuBar = new JMenuBar();
66 protected JMenuItem closeMenuItem = new JMenuItem();
68 protected JMenu webService = new JMenu();
70 protected JMenuItem webServiceNoServices;
72 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
74 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
76 protected JMenu sortByAnnotScore = new JMenu();
78 public JLabel statusBar = new JLabel();
80 protected JMenu outputTextboxMenu = new JMenu();
82 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
84 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
86 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
88 protected JMenuItem undoMenuItem = new JMenuItem();
90 protected JMenuItem redoMenuItem = new JMenuItem();
92 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
94 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
96 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
98 JMenuItem copy = new JMenuItem();
100 JMenuItem cut = new JMenuItem();
102 JMenu pasteMenu = new JMenu();
104 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
106 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
108 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
110 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
112 protected JCheckBoxMenuItem applyToAllGroups;
114 protected JMenu colourMenu = new JMenu();
116 protected JMenuItem textColour;
118 protected JCheckBoxMenuItem conservationMenuItem;
120 protected JMenuItem modifyConservation;
122 protected JCheckBoxMenuItem abovePIDThreshold;
124 protected JMenuItem modifyPID;
126 protected JMenuItem annotationColour;
128 protected JMenu sortByTreeMenu = new JMenu();
130 protected JMenu sort = new JMenu();
132 protected JMenuItem calculateTree = new JMenuItem();
134 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
136 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
138 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
140 protected JMenuItem showTranslation = new JMenuItem();
142 protected JMenuItem showReverse = new JMenuItem();
144 protected JMenuItem showReverseComplement = new JMenuItem();
146 protected JMenu showProducts = new JMenu();
148 protected JMenuItem runGroovy = new JMenuItem();
150 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
152 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
154 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
156 protected JPanel statusPanel = new JPanel();
158 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
160 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
162 protected JMenuItem showAllAlAnnotations = new JMenuItem();
164 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
166 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
168 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
170 protected JTabbedPane tabbedPane = new JTabbedPane();
172 protected JMenuItem reload = new JMenuItem();
174 protected JMenu formatMenu = new JMenu();
176 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
178 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
180 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
182 protected JMenuItem gatherViews = new JMenuItem();
184 protected JMenuItem expandViews = new JMenuItem();
186 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
188 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
190 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
192 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
194 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
196 protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
198 protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
202 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
204 private SequenceAnnotationOrder annotationSortOrder;
206 private boolean showAutoCalculatedAbove = false;
208 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
210 private SplitContainerI splitFrame;
217 setJMenuBar(alignFrameMenuBar);
219 // dynamically fill save as menu with available formats
220 for (String ff : FileFormats.getInstance().getWritableFormats(true))
222 JMenuItem item = new JMenuItem(ff);
224 item.addActionListener(new ActionListener()
227 public void actionPerformed(ActionEvent e)
229 outputText_actionPerformed(e);
233 outputTextboxMenu.add(item);
235 } catch (Exception e)
237 System.err.println(e.toString());
240 if (!Platform.isAMac())
242 closeMenuItem.setMnemonic('C');
243 outputTextboxMenu.setMnemonic('T');
244 undoMenuItem.setMnemonic('Z');
245 redoMenuItem.setMnemonic('0');
246 copy.setMnemonic('C');
247 cut.setMnemonic('U');
248 pasteMenu.setMnemonic('P');
249 reload.setMnemonic('R');
253 private void jbInit() throws Exception
257 JMenuItem saveAs = new JMenuItem(
258 MessageManager.getString("action.save_as"));
259 ActionListener al = new ActionListener()
262 public void actionPerformed(ActionEvent e)
264 saveAs_actionPerformed(e);
268 // FIXME getDefaultToolkit throws an exception in Headless mode
269 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
270 .getDefaultToolkit().getMenuShortcutKeyMask()
271 | KeyEvent.SHIFT_MASK, false);
272 addMenuActionAndAccelerator(keyStroke, saveAs, al);
274 closeMenuItem.setText(MessageManager.getString("action.close"));
275 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
276 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
277 al = new ActionListener()
280 public void actionPerformed(ActionEvent e)
282 closeMenuItem_actionPerformed(false);
285 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
287 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
288 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
289 JMenu annotationsMenu = new JMenu(
290 MessageManager.getString("action.annotations"));
291 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
292 colourMenu.setText(MessageManager.getString("action.colour"));
293 JMenu calculateMenu = new JMenu(
294 MessageManager.getString("action.calculate"));
295 webService.setText(MessageManager.getString("action.web_service"));
296 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
297 MessageManager.getString("action.select_all"));
298 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
299 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
300 al = new ActionListener()
303 public void actionPerformed(ActionEvent e)
305 selectAllSequenceMenuItem_actionPerformed(e);
308 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
310 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
311 MessageManager.getString("action.deselect_all"));
312 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
313 al = new ActionListener()
316 public void actionPerformed(ActionEvent e)
318 deselectAllSequenceMenuItem_actionPerformed(e);
321 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
323 JMenuItem invertSequenceMenuItem = new JMenuItem(
324 MessageManager.getString("action.invert_sequence_selection"));
325 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
326 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
327 al = new ActionListener()
330 public void actionPerformed(ActionEvent e)
332 invertSequenceMenuItem_actionPerformed(e);
335 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
337 JMenuItem grpsFromSelection = new JMenuItem(
338 MessageManager.getString("action.make_groups_selection"));
339 grpsFromSelection.addActionListener(new ActionListener()
342 public void actionPerformed(ActionEvent e)
344 makeGrpsFromSelection_actionPerformed(e);
347 JMenuItem expandAlignment = new JMenuItem(
348 MessageManager.getString("action.view_flanking_regions"));
349 expandAlignment.setToolTipText(MessageManager
350 .getString("label.view_flanking_regions"));
351 expandAlignment.addActionListener(new ActionListener()
354 public void actionPerformed(ActionEvent e)
359 JMenuItem remove2LeftMenuItem = new JMenuItem(
360 MessageManager.getString("action.remove_left"));
361 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
362 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
363 al = new ActionListener()
366 public void actionPerformed(ActionEvent e)
368 remove2LeftMenuItem_actionPerformed(e);
371 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
373 JMenuItem remove2RightMenuItem = new JMenuItem(
374 MessageManager.getString("action.remove_right"));
375 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
376 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
377 al = new ActionListener()
380 public void actionPerformed(ActionEvent e)
382 remove2RightMenuItem_actionPerformed(e);
385 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
387 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
388 MessageManager.getString("action.remove_empty_columns"));
389 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
390 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
391 al = new ActionListener()
394 public void actionPerformed(ActionEvent e)
396 removeGappedColumnMenuItem_actionPerformed(e);
399 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
401 JMenuItem removeAllGapsMenuItem = new JMenuItem(
402 MessageManager.getString("action.remove_all_gaps"));
403 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
404 .getDefaultToolkit().getMenuShortcutKeyMask()
405 | KeyEvent.SHIFT_MASK, false);
406 al = new ActionListener()
409 public void actionPerformed(ActionEvent e)
411 removeAllGapsMenuItem_actionPerformed(e);
414 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
416 JMenuItem justifyLeftMenuItem = new JMenuItem(
417 MessageManager.getString("action.left_justify_alignment"));
418 justifyLeftMenuItem.addActionListener(new ActionListener()
421 public void actionPerformed(ActionEvent e)
423 justifyLeftMenuItem_actionPerformed(e);
426 JMenuItem justifyRightMenuItem = new JMenuItem(
427 MessageManager.getString("action.right_justify_alignment"));
428 justifyRightMenuItem.addActionListener(new ActionListener()
431 public void actionPerformed(ActionEvent e)
433 justifyRightMenuItem_actionPerformed(e);
436 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
437 viewBoxesMenuItem.setState(true);
438 viewBoxesMenuItem.addActionListener(new ActionListener()
441 public void actionPerformed(ActionEvent e)
443 viewBoxesMenuItem_actionPerformed(e);
446 viewTextMenuItem.setText(MessageManager.getString("action.text"));
447 viewTextMenuItem.setState(true);
448 viewTextMenuItem.addActionListener(new ActionListener()
451 public void actionPerformed(ActionEvent e)
453 viewTextMenuItem_actionPerformed(e);
456 showNonconservedMenuItem.setText(MessageManager
457 .getString("label.show_non_conserved"));
458 showNonconservedMenuItem.setState(false);
459 showNonconservedMenuItem.addActionListener(new ActionListener()
462 public void actionPerformed(ActionEvent e)
464 showUnconservedMenuItem_actionPerformed(e);
467 JMenuItem sortPairwiseMenuItem = new JMenuItem(
468 MessageManager.getString("action.by_pairwise_id"));
469 sortPairwiseMenuItem.addActionListener(new ActionListener()
472 public void actionPerformed(ActionEvent e)
474 sortPairwiseMenuItem_actionPerformed(e);
477 JMenuItem sortIDMenuItem = new JMenuItem(
478 MessageManager.getString("action.by_id"));
479 sortIDMenuItem.addActionListener(new ActionListener()
482 public void actionPerformed(ActionEvent e)
484 sortIDMenuItem_actionPerformed(e);
487 JMenuItem sortLengthMenuItem = new JMenuItem(
488 MessageManager.getString("action.by_length"));
489 sortLengthMenuItem.addActionListener(new ActionListener()
492 public void actionPerformed(ActionEvent e)
494 sortLengthMenuItem_actionPerformed(e);
497 JMenuItem sortGroupMenuItem = new JMenuItem(
498 MessageManager.getString("action.by_group"));
499 sortGroupMenuItem.addActionListener(new ActionListener()
502 public void actionPerformed(ActionEvent e)
504 sortGroupMenuItem_actionPerformed(e);
508 JMenuItem removeRedundancyMenuItem = new JMenuItem(
509 MessageManager.getString("action.remove_redundancy"));
510 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
511 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
512 al = new ActionListener()
515 public void actionPerformed(ActionEvent e)
517 removeRedundancyMenuItem_actionPerformed(e);
520 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
522 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
523 MessageManager.getString("action.pairwise_alignment"));
524 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
527 public void actionPerformed(ActionEvent e)
529 pairwiseAlignmentMenuItem_actionPerformed(e);
533 this.getContentPane().setLayout(new BorderLayout());
534 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
535 statusBar.setBackground(Color.white);
536 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
537 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
538 statusBar.setText(MessageManager.getString("label.status_bar"));
539 outputTextboxMenu.setText(MessageManager
540 .getString("label.out_to_textbox"));
542 annotationPanelMenuItem.setActionCommand("");
543 annotationPanelMenuItem.setText(MessageManager
544 .getString("label.show_annotations"));
545 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
547 annotationPanelMenuItem.addActionListener(new ActionListener()
550 public void actionPerformed(ActionEvent e)
552 annotationPanelMenuItem_actionPerformed(e);
555 showAllAlAnnotations.setText(MessageManager
556 .getString("label.show_all_al_annotations"));
557 final boolean isAnnotationPanelShown = annotationPanelMenuItem
559 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
560 showAllAlAnnotations.addActionListener(new ActionListener()
563 public void actionPerformed(ActionEvent e)
565 showAllAnnotations_actionPerformed(false, true);
568 hideAllAlAnnotations.setText(MessageManager
569 .getString("label.hide_all_al_annotations"));
570 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
571 hideAllAlAnnotations.addActionListener(new ActionListener()
574 public void actionPerformed(ActionEvent e)
576 hideAllAnnotations_actionPerformed(false, true);
579 showAllSeqAnnotations.setText(MessageManager
580 .getString("label.show_all_seq_annotations"));
581 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
582 showAllSeqAnnotations.addActionListener(new ActionListener()
585 public void actionPerformed(ActionEvent e)
587 showAllAnnotations_actionPerformed(true, false);
590 hideAllSeqAnnotations.setText(MessageManager
591 .getString("label.hide_all_seq_annotations"));
592 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
593 hideAllSeqAnnotations.addActionListener(new ActionListener()
596 public void actionPerformed(ActionEvent e)
598 hideAllAnnotations_actionPerformed(true, false);
601 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
602 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
603 SequenceAnnotationOrder.NONE.name()));
604 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
605 MessageManager.getString("label.sort_annotations_by_sequence"));
606 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
607 MessageManager.getString("label.sort_annotations_by_label"));
610 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
611 sortAnnBySequence.addActionListener(new ActionListener()
614 public void actionPerformed(ActionEvent e)
616 boolean newState = sortAnnBySequence.getState();
617 sortAnnByLabel.setSelected(false);
618 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
619 : SequenceAnnotationOrder.NONE);
620 sortAnnotations_actionPerformed();
624 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
625 sortAnnByLabel.addActionListener(new ActionListener()
628 public void actionPerformed(ActionEvent e)
630 boolean newState = sortAnnByLabel.getState();
631 sortAnnBySequence.setSelected(false);
632 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
633 : SequenceAnnotationOrder.NONE);
634 sortAnnotations_actionPerformed();
637 colourTextMenuItem = new JCheckBoxMenuItem(
639 .getString("label.colour_text"));
640 colourTextMenuItem.addActionListener(new ActionListener()
643 public void actionPerformed(ActionEvent e)
645 colourTextMenuItem_actionPerformed(e);
649 JMenuItem htmlMenuItem = new JMenuItem(
650 MessageManager.getString("label.html"));
651 htmlMenuItem.addActionListener(new ActionListener()
654 public void actionPerformed(ActionEvent e)
656 htmlMenuItem_actionPerformed(e);
660 JMenuItem createBioJS = new JMenuItem(
661 MessageManager.getString("label.biojs_html_export"));
662 createBioJS.addActionListener(new java.awt.event.ActionListener()
665 public void actionPerformed(ActionEvent e)
667 bioJSMenuItem_actionPerformed(e);
671 JMenuItem overviewMenuItem = new JMenuItem(
672 MessageManager.getString("label.overview_window"));
673 overviewMenuItem.addActionListener(new ActionListener()
676 public void actionPerformed(ActionEvent e)
678 overviewMenuItem_actionPerformed(e);
682 undoMenuItem.setEnabled(false);
683 undoMenuItem.setText(MessageManager.getString("action.undo"));
684 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
685 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
686 al = new ActionListener()
689 public void actionPerformed(ActionEvent e)
691 undoMenuItem_actionPerformed(e);
694 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
696 redoMenuItem.setEnabled(false);
697 redoMenuItem.setText(MessageManager.getString("action.redo"));
698 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
699 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
700 al = new ActionListener()
703 public void actionPerformed(ActionEvent e)
705 redoMenuItem_actionPerformed(e);
708 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
710 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
711 wrapMenuItem.addActionListener(new ActionListener()
714 public void actionPerformed(ActionEvent e)
716 wrapMenuItem_actionPerformed(e);
720 JMenuItem printMenuItem = new JMenuItem(
721 MessageManager.getString("action.print"));
722 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
723 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
724 al = new ActionListener()
727 public void actionPerformed(ActionEvent e)
729 printMenuItem_actionPerformed(e);
732 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
735 .setText(MessageManager.getString("action.show_gaps"));
736 renderGapsMenuItem.setState(true);
737 renderGapsMenuItem.addActionListener(new ActionListener()
740 public void actionPerformed(ActionEvent e)
742 renderGapsMenuItem_actionPerformed(e);
746 JMenuItem findMenuItem = new JMenuItem(
747 MessageManager.getString("action.find"));
748 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
749 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
750 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
751 MessageManager.getString("label.find_tip")));
752 al = new ActionListener()
755 public void actionPerformed(ActionEvent e)
757 findMenuItem_actionPerformed(e);
760 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
762 showSeqFeatures.setText(MessageManager
763 .getString("label.show_sequence_features"));
764 showSeqFeatures.addActionListener(new ActionListener()
767 public void actionPerformed(ActionEvent actionEvent)
769 showSeqFeatures_actionPerformed(actionEvent);
773 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
774 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
775 * void actionPerformed(ActionEvent actionEvent) {
776 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
778 showDbRefsMenuitem.setText(MessageManager
779 .getString("label.show_database_refs"));
780 showDbRefsMenuitem.addActionListener(new ActionListener()
784 public void actionPerformed(ActionEvent e)
786 showDbRefs_actionPerformed(e);
790 showNpFeatsMenuitem.setText(MessageManager
791 .getString("label.show_non_positional_features"));
792 showNpFeatsMenuitem.addActionListener(new ActionListener()
796 public void actionPerformed(ActionEvent e)
798 showNpFeats_actionPerformed(e);
802 showGroupConservation.setText(MessageManager
803 .getString("label.group_conservation"));
804 showGroupConservation.addActionListener(new ActionListener()
808 public void actionPerformed(ActionEvent e)
810 showGroupConservation_actionPerformed(e);
815 showGroupConsensus.setText(MessageManager
816 .getString("label.group_consensus"));
817 showGroupConsensus.addActionListener(new ActionListener()
821 public void actionPerformed(ActionEvent e)
823 showGroupConsensus_actionPerformed(e);
827 showConsensusHistogram.setText(MessageManager
828 .getString("label.show_consensus_histogram"));
829 showConsensusHistogram.addActionListener(new ActionListener()
833 public void actionPerformed(ActionEvent e)
835 showConsensusHistogram_actionPerformed(e);
839 showSequenceLogo.setText(MessageManager
840 .getString("label.show_consensus_logo"));
841 showSequenceLogo.addActionListener(new ActionListener()
845 public void actionPerformed(ActionEvent e)
847 showSequenceLogo_actionPerformed(e);
851 normaliseSequenceLogo.setText(MessageManager
852 .getString("label.norm_consensus_logo"));
853 normaliseSequenceLogo.addActionListener(new ActionListener()
857 public void actionPerformed(ActionEvent e)
859 normaliseSequenceLogo_actionPerformed(e);
863 applyAutoAnnotationSettings.setText(MessageManager
864 .getString("label.apply_all_groups"));
865 applyAutoAnnotationSettings.setState(false);
866 applyAutoAnnotationSettings.setVisible(true);
867 applyAutoAnnotationSettings.addActionListener(new ActionListener()
870 public void actionPerformed(ActionEvent e)
872 applyAutoAnnotationSettings_actionPerformed(e);
876 ButtonGroup buttonGroup = new ButtonGroup();
877 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
878 MessageManager.getString("label.show_first"));
879 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
880 MessageManager.getString("label.show_last"));
881 buttonGroup.add(showAutoFirst);
882 buttonGroup.add(showAutoLast);
883 final boolean autoFirst = Cache.getDefault(
884 Preferences.SHOW_AUTOCALC_ABOVE, false);
885 showAutoFirst.setSelected(autoFirst);
886 setShowAutoCalculatedAbove(autoFirst);
887 showAutoFirst.addActionListener(new ActionListener()
890 public void actionPerformed(ActionEvent e)
892 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
893 sortAnnotations_actionPerformed();
896 showAutoLast.setSelected(!showAutoFirst.isSelected());
897 showAutoLast.addActionListener(new ActionListener()
900 public void actionPerformed(ActionEvent e)
902 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
903 sortAnnotations_actionPerformed();
907 JMenuItem deleteGroups = new JMenuItem(
908 MessageManager.getString("action.undefine_groups"));
909 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
910 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
911 al = new ActionListener()
914 public void actionPerformed(ActionEvent e)
916 deleteGroups_actionPerformed(e);
919 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
921 JMenuItem annotationColumn = new JMenuItem(
922 MessageManager.getString("action.select_by_annotation"));
923 annotationColumn.addActionListener(new ActionListener()
926 public void actionPerformed(ActionEvent e)
928 annotationColumn_actionPerformed(e);
932 JMenuItem createGroup = new JMenuItem(
933 MessageManager.getString("action.create_group"));
934 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
935 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
936 al = new ActionListener()
939 public void actionPerformed(ActionEvent e)
941 createGroup_actionPerformed(e);
944 addMenuActionAndAccelerator(keyStroke, createGroup, al);
946 JMenuItem unGroup = new JMenuItem(
947 MessageManager.getString("action.remove_group"));
948 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
949 .getDefaultToolkit().getMenuShortcutKeyMask()
950 | KeyEvent.SHIFT_MASK, false);
951 al = new ActionListener()
954 public void actionPerformed(ActionEvent e)
956 unGroup_actionPerformed(e);
959 addMenuActionAndAccelerator(keyStroke, unGroup, al);
961 copy.setText(MessageManager.getString("action.copy"));
962 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
963 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
965 al = new ActionListener()
968 public void actionPerformed(ActionEvent e)
970 copy_actionPerformed(e);
973 addMenuActionAndAccelerator(keyStroke, copy, al);
975 cut.setText(MessageManager.getString("action.cut"));
976 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
977 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
978 al = new ActionListener()
981 public void actionPerformed(ActionEvent e)
983 cut_actionPerformed(e);
986 addMenuActionAndAccelerator(keyStroke, cut, al);
988 JMenuItem delete = new JMenuItem(
989 MessageManager.getString("action.delete"));
990 delete.addActionListener(new ActionListener()
993 public void actionPerformed(ActionEvent e)
995 delete_actionPerformed(e);
999 pasteMenu.setText(MessageManager.getString("action.paste"));
1000 JMenuItem pasteNew = new JMenuItem(
1001 MessageManager.getString("label.to_new_alignment"));
1002 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1003 .getDefaultToolkit().getMenuShortcutKeyMask()
1004 | KeyEvent.SHIFT_MASK, false);
1005 al = new ActionListener()
1008 public void actionPerformed(ActionEvent e)
1010 pasteNew_actionPerformed(e);
1013 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1015 JMenuItem pasteThis = new JMenuItem(
1016 MessageManager.getString("label.to_this_alignment"));
1017 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1018 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1019 al = new ActionListener()
1022 public void actionPerformed(ActionEvent e)
1024 pasteThis_actionPerformed(e);
1027 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1029 JMenuItem createPNG = new JMenuItem("PNG");
1030 createPNG.addActionListener(new ActionListener()
1033 public void actionPerformed(ActionEvent e)
1038 createPNG.setActionCommand(MessageManager
1039 .getString("label.save_png_image"));
1041 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1042 font.addActionListener(new ActionListener()
1045 public void actionPerformed(ActionEvent e)
1047 font_actionPerformed(e);
1050 seqLimits.setText(MessageManager
1051 .getString("label.show_sequence_limits"));
1052 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1053 seqLimits.addActionListener(new ActionListener()
1056 public void actionPerformed(ActionEvent e)
1058 seqLimit_actionPerformed(e);
1061 JMenuItem epsFile = new JMenuItem("EPS");
1062 epsFile.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1071 JMenuItem createSVG = new JMenuItem("SVG");
1072 createSVG.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1081 JMenuItem loadTreeMenuItem = new JMenuItem(
1082 MessageManager.getString("label.load_associated_tree"));
1083 loadTreeMenuItem.setActionCommand(MessageManager
1084 .getString("label.load_tree_for_sequence_set"));
1085 loadTreeMenuItem.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 loadTreeMenuItem_actionPerformed(e);
1094 scaleAbove.setVisible(false);
1095 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1096 scaleAbove.addActionListener(new ActionListener()
1099 public void actionPerformed(ActionEvent e)
1101 scaleAbove_actionPerformed(e);
1104 scaleLeft.setVisible(false);
1105 scaleLeft.setSelected(true);
1106 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1107 scaleLeft.addActionListener(new ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 scaleLeft_actionPerformed(e);
1115 scaleRight.setVisible(false);
1116 scaleRight.setSelected(true);
1117 scaleRight.setText(MessageManager.getString("action.scale_right"));
1118 scaleRight.addActionListener(new ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 scaleRight_actionPerformed(e);
1126 centreColumnLabelsMenuItem.setVisible(true);
1127 centreColumnLabelsMenuItem.setState(false);
1128 centreColumnLabelsMenuItem.setText(MessageManager
1129 .getString("label.centre_column_labels"));
1130 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 centreColumnLabels_actionPerformed(e);
1138 followHighlightMenuItem.setVisible(true);
1139 followHighlightMenuItem.setState(true);
1140 followHighlightMenuItem.setText(MessageManager
1141 .getString("label.automatic_scrolling"));
1142 followHighlightMenuItem.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 followHighlight_actionPerformed();
1154 .setText(MessageManager.getString("action.by_tree_order"));
1155 sort.setText(MessageManager.getString("action.sort"));
1156 sort.addMenuListener(new MenuListener()
1159 public void menuSelected(MenuEvent e)
1161 buildTreeSortMenu();
1165 public void menuDeselected(MenuEvent e)
1170 public void menuCanceled(MenuEvent e)
1174 sortByAnnotScore.setText(MessageManager
1175 .getString("label.sort_by_score"));
1176 sort.add(sortByAnnotScore);
1177 sort.addMenuListener(new javax.swing.event.MenuListener()
1181 public void menuCanceled(MenuEvent e)
1186 public void menuDeselected(MenuEvent e)
1191 public void menuSelected(MenuEvent e)
1193 buildSortByAnnotationScoresMenu();
1196 sortByAnnotScore.setVisible(false);
1198 calculateTree.setText(MessageManager
1199 .getString("action.calculate_tree_pca"));
1201 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1202 padGapsMenuitem.setState(jalview.bin.Cache
1203 .getDefault("PAD_GAPS", false));
1204 padGapsMenuitem.addActionListener(new ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 padGapsMenuitem_actionPerformed(e);
1212 JMenuItem vamsasStore = new JMenuItem(
1213 MessageManager.getString("label.vamsas_store"));
1214 vamsasStore.setVisible(false);
1215 vamsasStore.addActionListener(new ActionListener()
1218 public void actionPerformed(ActionEvent e)
1220 vamsasStore_actionPerformed(e);
1223 showTranslation.setText(MessageManager
1224 .getString("label.translate_cDNA"));
1225 showTranslation.addActionListener(new ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 showTranslation_actionPerformed(e);
1233 showReverse.setText(MessageManager.getString("label.reverse"));
1234 showReverse.addActionListener(new ActionListener()
1237 public void actionPerformed(ActionEvent e)
1239 showReverse_actionPerformed(false);
1242 showReverseComplement.setText(MessageManager
1243 .getString("label.reverse_complement"));
1244 showReverseComplement.addActionListener(new ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 showReverse_actionPerformed(true);
1253 JMenuItem extractScores = new JMenuItem(
1254 MessageManager.getString("label.extract_scores"));
1255 extractScores.addActionListener(new ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 extractScores_actionPerformed(e);
1263 extractScores.setVisible(true);
1264 // JBPNote: TODO: make gui for regex based score extraction
1266 // for show products actions see AlignFrame.canShowProducts
1267 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1269 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1270 runGroovy.setToolTipText(MessageManager
1271 .getString("label.run_groovy_tip"));
1272 runGroovy.addActionListener(new ActionListener()
1275 public void actionPerformed(ActionEvent e)
1277 runGroovy_actionPerformed();
1281 JMenuItem openFeatureSettings = new JMenuItem(
1282 MessageManager.getString("action.feature_settings"));
1283 openFeatureSettings.addActionListener(new ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 featureSettings_actionPerformed(e);
1291 JMenuItem fetchSequence = new JMenuItem(
1292 MessageManager.getString("label.fetch_sequences"));
1293 fetchSequence.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 fetchSequence_actionPerformed(e);
1302 JMenuItem associatedData = new JMenuItem(
1303 MessageManager.getString("label.load_features_annotations"));
1304 associatedData.addActionListener(new ActionListener()
1307 public void actionPerformed(ActionEvent e)
1309 associatedData_actionPerformed(e);
1312 autoCalculate.setText(MessageManager
1313 .getString("label.autocalculate_consensus"));
1314 autoCalculate.setState(jalview.bin.Cache.getDefault(
1315 "AUTO_CALC_CONSENSUS", true));
1316 autoCalculate.addActionListener(new ActionListener()
1319 public void actionPerformed(ActionEvent e)
1321 autoCalculate_actionPerformed(e);
1324 sortByTree.setText(MessageManager
1325 .getString("label.sort_alignment_new_tree"));
1327 .setToolTipText("<html>"
1329 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1331 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1332 sortByTree.addActionListener(new ActionListener()
1335 public void actionPerformed(ActionEvent e)
1337 sortByTreeOption_actionPerformed(e);
1341 listenToViewSelections.setText(MessageManager
1342 .getString("label.listen_for_selections"));
1343 listenToViewSelections
1344 .setToolTipText("<html>"
1346 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1347 listenToViewSelections.setState(false);
1348 listenToViewSelections.addActionListener(new ActionListener()
1351 public void actionPerformed(ActionEvent e)
1353 listenToViewSelections_actionPerformed(e);
1357 JMenu addSequenceMenu = new JMenu(
1358 MessageManager.getString("label.add_sequences"));
1359 JMenuItem addFromFile = new JMenuItem(
1360 MessageManager.getString("label.from_file"));
1361 addFromFile.addActionListener(new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 addFromFile_actionPerformed(e);
1369 JMenuItem addFromText = new JMenuItem(
1370 MessageManager.getString("label.from_textbox"));
1371 addFromText.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 addFromText_actionPerformed(e);
1379 JMenuItem addFromURL = new JMenuItem(
1380 MessageManager.getString("label.from_url"));
1381 addFromURL.addActionListener(new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 addFromURL_actionPerformed(e);
1389 JMenuItem exportFeatures = new JMenuItem(
1390 MessageManager.getString("label.export_features"));
1391 exportFeatures.addActionListener(new ActionListener()
1394 public void actionPerformed(ActionEvent e)
1396 exportFeatures_actionPerformed(e);
1399 JMenuItem exportAnnotations = new JMenuItem(
1400 MessageManager.getString("label.export_annotations"));
1401 exportAnnotations.addActionListener(new ActionListener()
1404 public void actionPerformed(ActionEvent e)
1406 exportAnnotations_actionPerformed(e);
1409 statusPanel.setLayout(new GridLayout());
1410 JMenuItem showAllSeqs = new JMenuItem(
1411 MessageManager.getString("label.all_sequences"));
1412 showAllSeqs.setToolTipText(MessageManager
1413 .getString("label.toggle_sequence_visibility"));
1414 showAllSeqs.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent e)
1419 showAllSeqs_actionPerformed(e);
1422 JMenuItem showAllColumns = new JMenuItem(
1423 MessageManager.getString("label.all_columns"));
1424 showAllColumns.setToolTipText(MessageManager
1425 .getString("label.toggle_columns_visibility"));
1426 showAllColumns.addActionListener(new ActionListener()
1429 public void actionPerformed(ActionEvent e)
1431 showAllColumns_actionPerformed(e);
1434 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1435 JMenuItem hideSelSequences = new JMenuItem(
1436 MessageManager.getString("label.selected_sequences"));
1437 hideSelSequences.setToolTipText(MessageManager
1438 .getString("label.toggle_sequence_visibility"));
1439 hideSelSequences.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent e)
1444 hideSelSequences_actionPerformed(e);
1447 JMenuItem hideSelColumns = new JMenuItem(
1448 MessageManager.getString("label.selected_columns"));
1449 hideSelColumns.setToolTipText(MessageManager
1450 .getString("label.toggle_columns_visibility"));
1451 hideSelColumns.addActionListener(new ActionListener()
1454 public void actionPerformed(ActionEvent e)
1456 hideSelColumns_actionPerformed(e);
1459 JMenuItem hideAllSelection = new JMenuItem(
1460 MessageManager.getString("label.selected_region"));
1461 hideAllSelection.addActionListener(new ActionListener()
1464 public void actionPerformed(ActionEvent e)
1466 hideAllSelection_actionPerformed(e);
1469 // TODO: should be hidden if no selection exists.
1470 JMenuItem hideAllButSelection = new JMenuItem(
1471 MessageManager.getString("label.all_but_selected_region"));
1472 hideAllButSelection.addActionListener(new ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 hideAllButSelection_actionPerformed(e);
1480 JMenuItem showAllhidden = new JMenuItem(
1481 MessageManager.getString("label.all_sequences_columns"));
1482 showAllhidden.setToolTipText(MessageManager
1483 .getString("label.toggles_visibility_hidden_selected_regions"));
1484 showAllhidden.addActionListener(new ActionListener()
1487 public void actionPerformed(ActionEvent e)
1489 showAllhidden_actionPerformed(e);
1492 hiddenMarkers.setText(MessageManager
1493 .getString("action.show_hidden_markers"));
1494 hiddenMarkers.addActionListener(new ActionListener()
1497 public void actionPerformed(ActionEvent e)
1499 hiddenMarkers_actionPerformed(e);
1503 JMenuItem invertColSel = new JMenuItem(
1504 MessageManager.getString("action.invert_column_selection"));
1505 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1506 .getDefaultToolkit().getMenuShortcutKeyMask()
1507 | KeyEvent.ALT_MASK, false);
1508 al = new ActionListener()
1511 public void actionPerformed(ActionEvent e)
1513 invertColSel_actionPerformed(e);
1516 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1518 showComplementMenuItem.setVisible(false);
1519 showComplementMenuItem.addActionListener(new ActionListener()
1522 public void actionPerformed(ActionEvent e)
1524 showComplement_actionPerformed(showComplementMenuItem.getState());
1528 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1531 public void stateChanged(ChangeEvent evt)
1533 JTabbedPane pane = (JTabbedPane) evt.getSource();
1534 int sel = pane.getSelectedIndex();
1535 tabSelectionChanged(sel);
1538 tabbedPane.addMouseListener(new MouseAdapter()
1541 public void mousePressed(MouseEvent e)
1543 if (e.isPopupTrigger()) // Mac
1545 tabbedPane_mousePressed(e);
1550 public void mouseReleased(MouseEvent e)
1552 if (e.isPopupTrigger()) // Windows
1554 tabbedPane_mousePressed(e);
1558 tabbedPane.addFocusListener(new FocusAdapter()
1561 public void focusGained(FocusEvent e)
1563 tabbedPane_focusGained(e);
1567 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1568 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1569 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1570 al = new ActionListener()
1573 public void actionPerformed(ActionEvent e)
1575 save_actionPerformed(e);
1578 addMenuActionAndAccelerator(keyStroke, save, al);
1580 reload.setEnabled(false);
1581 reload.setText(MessageManager.getString("action.reload"));
1582 reload.addActionListener(new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 reload_actionPerformed(e);
1591 JMenuItem newView = new JMenuItem(
1592 MessageManager.getString("action.new_view"));
1593 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1594 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1595 al = new ActionListener()
1598 public void actionPerformed(ActionEvent e)
1600 newView_actionPerformed(e);
1603 addMenuActionAndAccelerator(keyStroke, newView, al);
1605 tabbedPane.setToolTipText("<html><i>"
1606 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1609 formatMenu.setText(MessageManager.getString("action.format"));
1610 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1612 idRightAlign.setText(MessageManager
1613 .getString("label.right_align_sequence_id"));
1614 idRightAlign.addActionListener(new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 idRightAlign_actionPerformed(e);
1623 gatherViews.setEnabled(false);
1624 gatherViews.setText(MessageManager.getString("action.gather_views"));
1625 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1626 al = new ActionListener()
1629 public void actionPerformed(ActionEvent e)
1631 gatherViews_actionPerformed(e);
1634 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1636 expandViews.setEnabled(false);
1637 expandViews.setText(MessageManager.getString("action.expand_views"));
1638 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1639 al = new ActionListener()
1642 public void actionPerformed(ActionEvent e)
1644 expandViews_actionPerformed(e);
1647 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1649 JMenuItem pageSetup = new JMenuItem(
1650 MessageManager.getString("action.page_setup"));
1651 pageSetup.addActionListener(new ActionListener()
1654 public void actionPerformed(ActionEvent e)
1656 pageSetup_actionPerformed(e);
1659 JMenuItem alignmentProperties = new JMenuItem(
1660 MessageManager.getString("label.alignment_props"));
1661 alignmentProperties.addActionListener(new ActionListener()
1664 public void actionPerformed(ActionEvent actionEvent)
1666 alignmentProperties();
1669 JMenuItem selectHighlighted = new JMenuItem(
1670 MessageManager.getString("action.select_highlighted_columns"));
1671 selectHighlighted.setToolTipText(MessageManager
1672 .getString("tooltip.select_highlighted_columns"));
1673 al = new ActionListener()
1676 public void actionPerformed(ActionEvent actionEvent)
1678 selectHighlightedColumns_actionPerformed(actionEvent);
1681 selectHighlighted.addActionListener(al);
1682 JMenu tooltipSettingsMenu = new JMenu(
1683 MessageManager.getString("label.sequence_id_tooltip"));
1684 JMenu autoAnnMenu = new JMenu(
1685 MessageManager.getString("label.autocalculated_annotation"));
1687 JMenu exportImageMenu = new JMenu(
1688 MessageManager.getString("label.export_image"));
1689 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1690 alignFrameMenuBar.add(fileMenu);
1691 alignFrameMenuBar.add(editMenu);
1692 alignFrameMenuBar.add(selectMenu);
1693 alignFrameMenuBar.add(viewMenu);
1694 alignFrameMenuBar.add(annotationsMenu);
1695 alignFrameMenuBar.add(formatMenu);
1696 alignFrameMenuBar.add(colourMenu);
1697 alignFrameMenuBar.add(calculateMenu);
1698 alignFrameMenuBar.add(webService);
1700 fileMenu.add(fetchSequence);
1701 fileMenu.add(addSequenceMenu);
1702 fileMenu.add(reload);
1703 fileMenu.addSeparator();
1704 fileMenu.add(vamsasStore);
1706 fileMenu.add(saveAs);
1707 fileMenu.add(outputTextboxMenu);
1708 fileMenu.add(pageSetup);
1709 fileMenu.add(printMenuItem);
1710 fileMenu.addSeparator();
1711 fileMenu.add(exportImageMenu);
1712 fileMenu.add(exportFeatures);
1713 fileMenu.add(exportAnnotations);
1714 fileMenu.add(loadTreeMenuItem);
1715 fileMenu.add(associatedData);
1716 fileMenu.addSeparator();
1717 fileMenu.add(closeMenuItem);
1719 pasteMenu.add(pasteNew);
1720 pasteMenu.add(pasteThis);
1721 editMenu.add(undoMenuItem);
1722 editMenu.add(redoMenuItem);
1725 editMenu.add(pasteMenu);
1726 editMenu.add(delete);
1727 editMenu.addSeparator();
1728 editMenu.add(remove2LeftMenuItem);
1729 editMenu.add(remove2RightMenuItem);
1730 editMenu.add(removeGappedColumnMenuItem);
1731 editMenu.add(removeAllGapsMenuItem);
1732 editMenu.add(removeRedundancyMenuItem);
1733 editMenu.addSeparator();
1734 // dont add these yet in the CVS build - they cannot be undone!
1735 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1736 // editMenu.add(justifyLeftMenuItem);
1737 // editMenu.add(justifyRightMenuItem);
1738 // editMenu.addSeparator();
1739 editMenu.add(padGapsMenuitem);
1741 showMenu.add(showAllColumns);
1742 showMenu.add(showAllSeqs);
1743 showMenu.add(showAllhidden);
1744 hideMenu.add(hideSelColumns);
1745 hideMenu.add(hideSelSequences);
1746 hideMenu.add(hideAllSelection);
1747 hideMenu.add(hideAllButSelection);
1748 viewMenu.add(newView);
1749 viewMenu.add(expandViews);
1750 viewMenu.add(gatherViews);
1751 viewMenu.addSeparator();
1752 viewMenu.add(showMenu);
1753 viewMenu.add(hideMenu);
1754 viewMenu.add(showComplementMenuItem);
1755 viewMenu.addSeparator();
1756 viewMenu.add(followHighlightMenuItem);
1757 viewMenu.addSeparator();
1758 viewMenu.add(showSeqFeatures);
1759 // viewMenu.add(showSeqFeaturesHeight);
1760 viewMenu.add(openFeatureSettings);
1761 tooltipSettingsMenu.add(showDbRefsMenuitem);
1762 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1763 viewMenu.add(tooltipSettingsMenu);
1764 viewMenu.addSeparator();
1765 viewMenu.add(alignmentProperties);
1766 viewMenu.addSeparator();
1767 viewMenu.add(overviewMenuItem);
1769 annotationsMenu.add(annotationPanelMenuItem);
1770 annotationsMenu.addSeparator();
1771 annotationsMenu.add(showAllAlAnnotations);
1772 annotationsMenu.add(hideAllAlAnnotations);
1773 annotationsMenu.addSeparator();
1774 annotationsMenu.add(showAllSeqAnnotations);
1775 annotationsMenu.add(hideAllSeqAnnotations);
1776 annotationsMenu.add(sortAnnBySequence);
1777 annotationsMenu.add(sortAnnByLabel);
1778 annotationsMenu.addSeparator();
1779 autoAnnMenu.add(showAutoFirst);
1780 autoAnnMenu.add(showAutoLast);
1781 autoAnnMenu.addSeparator();
1782 autoAnnMenu.add(applyAutoAnnotationSettings);
1783 autoAnnMenu.add(showConsensusHistogram);
1784 autoAnnMenu.add(showSequenceLogo);
1785 autoAnnMenu.add(normaliseSequenceLogo);
1786 autoAnnMenu.addSeparator();
1787 autoAnnMenu.add(showGroupConservation);
1788 autoAnnMenu.add(showGroupConsensus);
1789 annotationsMenu.add(autoAnnMenu);
1792 sort.add(sortIDMenuItem);
1793 sort.add(sortLengthMenuItem);
1794 sort.add(sortGroupMenuItem);
1795 sort.add(sortPairwiseMenuItem);
1796 sort.add(sortByTreeMenu);
1797 calculateMenu.add(sort);
1798 calculateMenu.add(calculateTree);
1799 calculateMenu.addSeparator();
1800 calculateMenu.add(pairwiseAlignmentMenuItem);
1801 calculateMenu.addSeparator();
1802 calculateMenu.add(showTranslation);
1803 calculateMenu.add(showReverse);
1804 calculateMenu.add(showReverseComplement);
1805 calculateMenu.add(showProducts);
1806 calculateMenu.add(autoCalculate);
1807 calculateMenu.add(sortByTree);
1808 calculateMenu.addSeparator();
1809 calculateMenu.add(expandAlignment);
1810 calculateMenu.add(extractScores);
1811 calculateMenu.addSeparator();
1812 calculateMenu.add(runGroovy);
1814 webServiceNoServices = new JMenuItem(
1815 MessageManager.getString("label.no_services"));
1816 webService.add(webServiceNoServices);
1817 exportImageMenu.add(htmlMenuItem);
1818 exportImageMenu.add(epsFile);
1819 exportImageMenu.add(createPNG);
1820 exportImageMenu.add(createBioJS);
1821 exportImageMenu.add(createSVG);
1822 addSequenceMenu.add(addFromFile);
1823 addSequenceMenu.add(addFromText);
1824 addSequenceMenu.add(addFromURL);
1825 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1826 statusPanel.add(statusBar, null);
1827 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1829 formatMenu.add(font);
1830 formatMenu.addSeparator();
1831 formatMenu.add(wrapMenuItem);
1832 formatMenu.add(scaleAbove);
1833 formatMenu.add(scaleLeft);
1834 formatMenu.add(scaleRight);
1835 formatMenu.add(seqLimits);
1836 formatMenu.add(idRightAlign);
1837 formatMenu.add(hiddenMarkers);
1838 formatMenu.add(viewBoxesMenuItem);
1839 formatMenu.add(viewTextMenuItem);
1840 formatMenu.add(colourTextMenuItem);
1841 formatMenu.add(renderGapsMenuItem);
1842 formatMenu.add(centreColumnLabelsMenuItem);
1843 formatMenu.add(showNonconservedMenuItem);
1844 selectMenu.add(findMenuItem);
1845 selectMenu.addSeparator();
1846 selectMenu.add(selectAllSequenceMenuItem);
1847 selectMenu.add(deselectAllSequenceMenuItem);
1848 selectMenu.add(invertSequenceMenuItem);
1849 selectMenu.add(invertColSel);
1850 selectMenu.add(createGroup);
1851 selectMenu.add(unGroup);
1852 selectMenu.add(grpsFromSelection);
1853 selectMenu.add(deleteGroups);
1854 selectMenu.add(annotationColumn);
1855 selectMenu.add(selectHighlighted);
1856 // TODO - determine if the listenToViewSelections button is needed : see bug
1858 // selectMenu.addSeparator();
1859 // selectMenu.add(listenToViewSelections);
1863 * Constructs the entries on the Colour menu (but does not add them to the
1866 protected void initColourMenu()
1868 applyToAllGroups = new JCheckBoxMenuItem(
1869 MessageManager.getString("label.apply_colour_to_all_groups"));
1870 applyToAllGroups.addActionListener(new ActionListener()
1873 public void actionPerformed(ActionEvent e)
1875 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1879 textColour = new JMenuItem(
1880 MessageManager.getString("label.text_colour"));
1881 textColour.addActionListener(new ActionListener()
1884 public void actionPerformed(ActionEvent e)
1886 textColour_actionPerformed();
1890 conservationMenuItem = new JCheckBoxMenuItem(
1891 MessageManager.getString("action.by_conservation"));
1892 conservationMenuItem.addActionListener(new ActionListener()
1895 public void actionPerformed(ActionEvent e)
1897 conservationMenuItem_actionPerformed(conservationMenuItem
1902 abovePIDThreshold = new JCheckBoxMenuItem(
1903 MessageManager.getString("label.above_identity_threshold"));
1904 abovePIDThreshold.addActionListener(new ActionListener()
1907 public void actionPerformed(ActionEvent e)
1909 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1912 modifyPID = new JMenuItem(
1913 MessageManager.getString("label.modify_identity_threshold"));
1914 modifyPID.addActionListener(new ActionListener()
1917 public void actionPerformed(ActionEvent e)
1919 modifyPID_actionPerformed();
1922 modifyConservation = new JMenuItem(
1924 .getString("label.modify_conservation_threshold"));
1925 modifyConservation.addActionListener(new ActionListener()
1928 public void actionPerformed(ActionEvent e)
1930 modifyConservation_actionPerformed();
1934 annotationColour = new JMenuItem(
1935 MessageManager.getString("action.by_annotation"));
1936 annotationColour.addActionListener(new ActionListener()
1939 public void actionPerformed(ActionEvent e)
1941 annotationColour_actionPerformed();
1946 protected void selectHighlightedColumns_actionPerformed(
1947 ActionEvent actionEvent)
1949 // TODO Auto-generated method stub
1954 * Generate the reverse sequence (or reverse complement if the flag is true)
1955 * and add it to the alignment
1959 protected void showReverse_actionPerformed(boolean complement)
1964 * Try to run script in a Groovy console, having first ensured that this
1965 * alignframe is set as currentAlignFrame in Desktop
1967 protected void runGroovy_actionPerformed()
1973 * Adds the given action listener and key accelerator to the given menu item.
1974 * Also saves in a lookup table to support lookup of action by key stroke.
1978 * @param actionListener
1980 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
1981 JMenuItem menuItem, ActionListener actionListener)
1983 menuItem.setAccelerator(keyStroke);
1984 accelerators.put(keyStroke, menuItem);
1985 menuItem.addActionListener(actionListener);
1989 * Action on clicking sort annotations by type.
1993 protected void sortAnnotations_actionPerformed()
1998 * Action on clicking Show all annotations.
2000 * @param forSequences
2001 * update sequence-related annotations
2002 * @param forAlignment
2003 * update non-sequence-related annotations
2005 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2006 boolean forAlignment)
2008 setAnnotationsVisibility(true, forSequences, forAlignment);
2012 * Action on clicking Hide all annotations.
2014 * @param forSequences
2015 * update sequence-related annotations
2016 * @param forAlignment
2017 * update non-sequence-related annotations
2019 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2020 boolean forAlignment)
2022 setAnnotationsVisibility(false, forSequences, forAlignment);
2026 * Set the visibility of annotations to true or false. Can act on
2027 * sequence-related annotations, or alignment-related, or both.
2030 * @param forSequences
2031 * update sequence-related annotations
2032 * @param forAlignment
2033 * update non-sequence-related annotations
2035 protected void setAnnotationsVisibility(boolean visible,
2036 boolean forSequences, boolean forAlignment)
2041 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2043 // TODO Auto-generated method stub
2047 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2049 // TODO Auto-generated method stub
2053 protected void showAllhidden_actionPerformed(ActionEvent e)
2055 // TODO Auto-generated method stub
2059 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2061 // TODO Auto-generated method stub
2065 protected void hideAllSelection_actionPerformed(ActionEvent e)
2067 // TODO Auto-generated method stub
2071 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2073 // TODO Auto-generated method stub
2077 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2079 // TODO Auto-generated method stub
2083 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2085 // TODO Auto-generated method stub
2089 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2091 // TODO Auto-generated method stub
2095 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2097 // TODO Auto-generated method stub
2101 protected void showGroupConservation_actionPerformed(ActionEvent e)
2103 // TODO Auto-generated method stub
2107 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2109 // TODO Auto-generated method stub
2113 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2115 // TODO Auto-generated method stub
2119 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2121 // TODO Auto-generated method stub
2125 protected void followHighlight_actionPerformed()
2127 // TODO Auto-generated method stub
2131 protected void showNpFeats_actionPerformed(ActionEvent e)
2133 // TODO Auto-generated method stub
2137 protected void showDbRefs_actionPerformed(ActionEvent e)
2139 // TODO Auto-generated method stub
2143 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2147 protected void buildSortByAnnotationScoresMenu()
2151 protected void extractScores_actionPerformed(ActionEvent e)
2155 protected void outputText_actionPerformed(ActionEvent e)
2159 public void addFromFile_actionPerformed(ActionEvent e)
2164 public void addFromText_actionPerformed(ActionEvent e)
2169 public void addFromURL_actionPerformed(ActionEvent e)
2174 public void exportFeatures_actionPerformed(ActionEvent e)
2179 public void exportAnnotations_actionPerformed(ActionEvent e)
2184 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2188 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2193 protected void closeMenuItem_actionPerformed(boolean b)
2197 protected void redoMenuItem_actionPerformed(ActionEvent e)
2201 protected void undoMenuItem_actionPerformed(ActionEvent e)
2205 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2209 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2213 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2217 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2221 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2225 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2229 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2233 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2237 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2241 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2245 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2249 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2253 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2257 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2261 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2265 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2269 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2273 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2277 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2281 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2285 protected void conservationMenuItem_actionPerformed(boolean selected)
2289 protected void printMenuItem_actionPerformed(ActionEvent e)
2293 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2297 protected void findMenuItem_actionPerformed(ActionEvent e)
2301 protected void abovePIDThreshold_actionPerformed(boolean selected)
2305 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2309 protected void deleteGroups_actionPerformed(ActionEvent e)
2313 protected void createGroup_actionPerformed(ActionEvent e)
2317 protected void unGroup_actionPerformed(ActionEvent e)
2321 protected void copy_actionPerformed(ActionEvent e)
2325 protected void cut_actionPerformed(ActionEvent e)
2329 protected void delete_actionPerformed(ActionEvent e)
2333 protected void pasteNew_actionPerformed(ActionEvent e)
2337 protected void pasteThis_actionPerformed(ActionEvent e)
2341 protected void applyToAllGroups_actionPerformed(boolean selected)
2345 public void createPNG(java.io.File f)
2349 protected void font_actionPerformed(ActionEvent e)
2353 protected void seqLimit_actionPerformed(ActionEvent e)
2357 public void seqDBRef_actionPerformed(ActionEvent e)
2362 public void createEPS(java.io.File f)
2366 public void createSVG(java.io.File f)
2371 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2377 * Template method to handle the 'load T-Coffee scores' menu event.
2379 * Subclasses override this method to provide a custom action.
2384 protected void loadScores_actionPerformed(ActionEvent event)
2389 protected void jpred_actionPerformed(ActionEvent e)
2393 protected void scaleAbove_actionPerformed(ActionEvent e)
2397 protected void scaleLeft_actionPerformed(ActionEvent e)
2401 protected void scaleRight_actionPerformed(ActionEvent e)
2405 protected void modifyPID_actionPerformed()
2409 protected void modifyConservation_actionPerformed()
2413 protected void saveAs_actionPerformed(ActionEvent e)
2417 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2421 public void vamsasStore_actionPerformed(ActionEvent e)
2426 public void vamsasLoad_actionPerformed(ActionEvent e)
2431 public void showTranslation_actionPerformed(ActionEvent e)
2436 public void featureSettings_actionPerformed(ActionEvent e)
2441 public void fetchSequence_actionPerformed(ActionEvent e)
2446 public void smoothFont_actionPerformed(ActionEvent e)
2451 public void annotationColour_actionPerformed()
2455 public void annotationColumn_actionPerformed(ActionEvent e)
2459 public void associatedData_actionPerformed(ActionEvent e)
2464 public void autoCalculate_actionPerformed(ActionEvent e)
2469 public void sortByTreeOption_actionPerformed(ActionEvent e)
2474 public void showAllSeqs_actionPerformed(ActionEvent e)
2479 public void showAllColumns_actionPerformed(ActionEvent e)
2484 public void hideSelSequences_actionPerformed(ActionEvent e)
2489 public void hideSelColumns_actionPerformed(ActionEvent e)
2494 public void hiddenMarkers_actionPerformed(ActionEvent e)
2499 public void findPdbId_actionPerformed(ActionEvent e)
2504 public void enterPdbId_actionPerformed(ActionEvent e)
2509 public void pdbFile_actionPerformed(ActionEvent e)
2514 public void invertColSel_actionPerformed(ActionEvent e)
2519 public void tabSelectionChanged(int sel)
2524 public void tabbedPane_mousePressed(MouseEvent e)
2529 public void tabbedPane_focusGained(FocusEvent e)
2534 public void save_actionPerformed(ActionEvent e)
2539 public void reload_actionPerformed(ActionEvent e)
2544 public void newView_actionPerformed(ActionEvent e)
2549 public void textColour_actionPerformed()
2554 public void idRightAlign_actionPerformed(ActionEvent e)
2559 public void expandViews_actionPerformed(ActionEvent e)
2564 public void gatherViews_actionPerformed(ActionEvent e)
2569 public void buildTreeSortMenu()
2574 public void pageSetup_actionPerformed(ActionEvent e)
2579 public void alignmentProperties()
2584 protected void expand_newalign(ActionEvent e)
2586 // TODO Auto-generated method stub
2590 protected boolean isShowAutoCalculatedAbove()
2592 return showAutoCalculatedAbove;
2595 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2597 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2600 protected SequenceAnnotationOrder getAnnotationSortOrder()
2602 return annotationSortOrder;
2605 protected void setAnnotationSortOrder(
2606 SequenceAnnotationOrder annotationSortOrder)
2608 this.annotationSortOrder = annotationSortOrder;
2611 public Map<KeyStroke, JMenuItem> getAccelerators()
2613 return this.accelerators;
2617 * Returns the selected index of the tabbed pane, or -1 if none selected
2618 * (including the case where the tabbed pane has not been made visible).
2622 public int getTabIndex()
2624 return tabbedPane.getSelectedIndex();
2627 public JPanel getStatusPanel()
2633 * Sets a reference to the containing split frame. Also makes the 'toggle
2634 * split view' menu item visible and checked.
2638 public void setSplitFrame(SplitContainerI sf)
2640 this.splitFrame = sf;
2643 this.showComplementMenuItem.setVisible(true);
2644 this.showComplementMenuItem.setState(true);
2648 public SplitContainerI getSplitViewContainer()
2650 return this.splitFrame;
2653 protected void showComplement_actionPerformed(boolean complement)
2657 protected void showInformationHistogram_actionPerformed(ActionEvent e)
2659 // TODO Auto-generated method stub
2663 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2665 // TODO Auto-generated method stub
2669 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2671 // TODO Auto-generated method stub