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 JRadioButtonMenuItem 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 JMenu calculateTree = new JMenu();
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 applyAutoAnnotationSettings = new JCheckBoxMenuItem();
198 private SequenceAnnotationOrder annotationSortOrder;
200 private boolean showAutoCalculatedAbove = false;
202 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
204 private SplitContainerI splitFrame;
211 setJMenuBar(alignFrameMenuBar);
213 // dynamically fill save as menu with available formats
214 for (String ff : FileFormats.getInstance().getWritableFormats(true))
216 JMenuItem item = new JMenuItem(ff);
218 item.addActionListener(new ActionListener()
221 public void actionPerformed(ActionEvent e)
223 outputText_actionPerformed(e);
227 outputTextboxMenu.add(item);
229 } catch (Exception e)
231 System.err.println(e.toString());
234 if (!Platform.isAMac())
236 closeMenuItem.setMnemonic('C');
237 outputTextboxMenu.setMnemonic('T');
238 undoMenuItem.setMnemonic('Z');
239 redoMenuItem.setMnemonic('0');
240 copy.setMnemonic('C');
241 cut.setMnemonic('U');
242 pasteMenu.setMnemonic('P');
243 reload.setMnemonic('R');
247 private void jbInit() throws Exception
251 JMenuItem saveAs = new JMenuItem(
252 MessageManager.getString("action.save_as"));
253 ActionListener al = new ActionListener()
256 public void actionPerformed(ActionEvent e)
258 saveAs_actionPerformed(e);
262 // FIXME getDefaultToolkit throws an exception in Headless mode
263 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
264 .getDefaultToolkit().getMenuShortcutKeyMask()
265 | KeyEvent.SHIFT_MASK, false);
266 addMenuActionAndAccelerator(keyStroke, saveAs, al);
268 closeMenuItem.setText(MessageManager.getString("action.close"));
269 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
270 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
271 al = new ActionListener()
274 public void actionPerformed(ActionEvent e)
276 closeMenuItem_actionPerformed(false);
279 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
281 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
282 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
283 JMenu annotationsMenu = new JMenu(
284 MessageManager.getString("action.annotations"));
285 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
286 colourMenu.setText(MessageManager.getString("action.colour"));
287 JMenu calculateMenu = new JMenu(
288 MessageManager.getString("action.calculate"));
289 webService.setText(MessageManager.getString("action.web_service"));
290 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
291 MessageManager.getString("action.select_all"));
292 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
293 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
294 al = new ActionListener()
297 public void actionPerformed(ActionEvent e)
299 selectAllSequenceMenuItem_actionPerformed(e);
302 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
304 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
305 MessageManager.getString("action.deselect_all"));
306 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
307 al = new ActionListener()
310 public void actionPerformed(ActionEvent e)
312 deselectAllSequenceMenuItem_actionPerformed(e);
315 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
317 JMenuItem invertSequenceMenuItem = new JMenuItem(
318 MessageManager.getString("action.invert_sequence_selection"));
319 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
320 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
321 al = new ActionListener()
324 public void actionPerformed(ActionEvent e)
326 invertSequenceMenuItem_actionPerformed(e);
329 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
331 JMenuItem grpsFromSelection = new JMenuItem(
332 MessageManager.getString("action.make_groups_selection"));
333 grpsFromSelection.addActionListener(new ActionListener()
336 public void actionPerformed(ActionEvent e)
338 makeGrpsFromSelection_actionPerformed(e);
341 JMenuItem expandAlignment = new JMenuItem(
342 MessageManager.getString("action.view_flanking_regions"));
343 expandAlignment.setToolTipText(MessageManager
344 .getString("label.view_flanking_regions"));
345 expandAlignment.addActionListener(new ActionListener()
348 public void actionPerformed(ActionEvent e)
353 JMenuItem remove2LeftMenuItem = new JMenuItem(
354 MessageManager.getString("action.remove_left"));
355 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
356 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
357 al = new ActionListener()
360 public void actionPerformed(ActionEvent e)
362 remove2LeftMenuItem_actionPerformed(e);
365 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
367 JMenuItem remove2RightMenuItem = new JMenuItem(
368 MessageManager.getString("action.remove_right"));
369 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
370 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
371 al = new ActionListener()
374 public void actionPerformed(ActionEvent e)
376 remove2RightMenuItem_actionPerformed(e);
379 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
381 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
382 MessageManager.getString("action.remove_empty_columns"));
383 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
384 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
385 al = new ActionListener()
388 public void actionPerformed(ActionEvent e)
390 removeGappedColumnMenuItem_actionPerformed(e);
393 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
395 JMenuItem removeAllGapsMenuItem = new JMenuItem(
396 MessageManager.getString("action.remove_all_gaps"));
397 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
398 .getDefaultToolkit().getMenuShortcutKeyMask()
399 | KeyEvent.SHIFT_MASK, false);
400 al = new ActionListener()
403 public void actionPerformed(ActionEvent e)
405 removeAllGapsMenuItem_actionPerformed(e);
408 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
410 JMenuItem justifyLeftMenuItem = new JMenuItem(
411 MessageManager.getString("action.left_justify_alignment"));
412 justifyLeftMenuItem.addActionListener(new ActionListener()
415 public void actionPerformed(ActionEvent e)
417 justifyLeftMenuItem_actionPerformed(e);
420 JMenuItem justifyRightMenuItem = new JMenuItem(
421 MessageManager.getString("action.right_justify_alignment"));
422 justifyRightMenuItem.addActionListener(new ActionListener()
425 public void actionPerformed(ActionEvent e)
427 justifyRightMenuItem_actionPerformed(e);
430 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
431 viewBoxesMenuItem.setState(true);
432 viewBoxesMenuItem.addActionListener(new ActionListener()
435 public void actionPerformed(ActionEvent e)
437 viewBoxesMenuItem_actionPerformed(e);
440 viewTextMenuItem.setText(MessageManager.getString("action.text"));
441 viewTextMenuItem.setState(true);
442 viewTextMenuItem.addActionListener(new ActionListener()
445 public void actionPerformed(ActionEvent e)
447 viewTextMenuItem_actionPerformed(e);
450 showNonconservedMenuItem.setText(MessageManager
451 .getString("label.show_non_conserved"));
452 showNonconservedMenuItem.setState(false);
453 showNonconservedMenuItem.addActionListener(new ActionListener()
456 public void actionPerformed(ActionEvent e)
458 showUnconservedMenuItem_actionPerformed(e);
461 JMenuItem sortPairwiseMenuItem = new JMenuItem(
462 MessageManager.getString("action.by_pairwise_id"));
463 sortPairwiseMenuItem.addActionListener(new ActionListener()
466 public void actionPerformed(ActionEvent e)
468 sortPairwiseMenuItem_actionPerformed(e);
471 JMenuItem sortIDMenuItem = new JMenuItem(
472 MessageManager.getString("action.by_id"));
473 sortIDMenuItem.addActionListener(new ActionListener()
476 public void actionPerformed(ActionEvent e)
478 sortIDMenuItem_actionPerformed(e);
481 JMenuItem sortLengthMenuItem = new JMenuItem(
482 MessageManager.getString("action.by_length"));
483 sortLengthMenuItem.addActionListener(new ActionListener()
486 public void actionPerformed(ActionEvent e)
488 sortLengthMenuItem_actionPerformed(e);
491 JMenuItem sortGroupMenuItem = new JMenuItem(
492 MessageManager.getString("action.by_group"));
493 sortGroupMenuItem.addActionListener(new ActionListener()
496 public void actionPerformed(ActionEvent e)
498 sortGroupMenuItem_actionPerformed(e);
502 JMenuItem removeRedundancyMenuItem = new JMenuItem(
503 MessageManager.getString("action.remove_redundancy"));
504 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
505 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
506 al = new ActionListener()
509 public void actionPerformed(ActionEvent e)
511 removeRedundancyMenuItem_actionPerformed(e);
514 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
516 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
517 MessageManager.getString("action.pairwise_alignment"));
518 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
521 public void actionPerformed(ActionEvent e)
523 pairwiseAlignmentMenuItem_actionPerformed(e);
526 JMenuItem PCAMenuItem = new JMenuItem(
527 MessageManager.getString("label.principal_component_analysis"));
528 PCAMenuItem.addActionListener(new ActionListener()
531 public void actionPerformed(ActionEvent e)
533 PCAMenuItem_actionPerformed(e);
536 JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
537 MessageManager.getString("label.average_distance_identity"));
538 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
541 public void actionPerformed(ActionEvent e)
543 averageDistanceTreeMenuItem_actionPerformed(e);
546 JMenuItem neighbourTreeMenuItem = new JMenuItem(
547 MessageManager.getString("label.neighbour_joining_identity"));
548 neighbourTreeMenuItem.addActionListener(new ActionListener()
551 public void actionPerformed(ActionEvent e)
553 neighbourTreeMenuItem_actionPerformed(e);
557 this.getContentPane().setLayout(new BorderLayout());
558 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
559 statusBar.setBackground(Color.white);
560 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
561 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
562 statusBar.setText(MessageManager.getString("label.status_bar"));
563 outputTextboxMenu.setText(MessageManager
564 .getString("label.out_to_textbox"));
567 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
568 MessageManager.getString("label.average_distance_blosum62"));
569 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
572 public void actionPerformed(ActionEvent e)
574 avTreeBlosumMenuItem_actionPerformed(e);
577 JMenuItem njTreeBlosumMenuItem = new JMenuItem(
578 MessageManager.getString("label.neighbour_blosum62"));
579 njTreeBlosumMenuItem.addActionListener(new ActionListener()
582 public void actionPerformed(ActionEvent e)
584 njTreeBlosumMenuItem_actionPerformed(e);
587 annotationPanelMenuItem.setActionCommand("");
588 annotationPanelMenuItem.setText(MessageManager
589 .getString("label.show_annotations"));
590 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
592 annotationPanelMenuItem.addActionListener(new ActionListener()
595 public void actionPerformed(ActionEvent e)
597 annotationPanelMenuItem_actionPerformed(e);
600 showAllAlAnnotations.setText(MessageManager
601 .getString("label.show_all_al_annotations"));
602 final boolean isAnnotationPanelShown = annotationPanelMenuItem
604 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
605 showAllAlAnnotations.addActionListener(new ActionListener()
608 public void actionPerformed(ActionEvent e)
610 showAllAnnotations_actionPerformed(false, true);
613 hideAllAlAnnotations.setText(MessageManager
614 .getString("label.hide_all_al_annotations"));
615 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
616 hideAllAlAnnotations.addActionListener(new ActionListener()
619 public void actionPerformed(ActionEvent e)
621 hideAllAnnotations_actionPerformed(false, true);
624 showAllSeqAnnotations.setText(MessageManager
625 .getString("label.show_all_seq_annotations"));
626 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
627 showAllSeqAnnotations.addActionListener(new ActionListener()
630 public void actionPerformed(ActionEvent e)
632 showAllAnnotations_actionPerformed(true, false);
635 hideAllSeqAnnotations.setText(MessageManager
636 .getString("label.hide_all_seq_annotations"));
637 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
638 hideAllSeqAnnotations.addActionListener(new ActionListener()
641 public void actionPerformed(ActionEvent e)
643 hideAllAnnotations_actionPerformed(true, false);
646 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
647 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
648 SequenceAnnotationOrder.NONE.name()));
649 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
650 MessageManager.getString("label.sort_annotations_by_sequence"));
651 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
652 MessageManager.getString("label.sort_annotations_by_label"));
655 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
656 sortAnnBySequence.addActionListener(new ActionListener()
659 public void actionPerformed(ActionEvent e)
661 boolean newState = sortAnnBySequence.getState();
662 sortAnnByLabel.setSelected(false);
663 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
664 : SequenceAnnotationOrder.NONE);
665 sortAnnotations_actionPerformed();
669 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
670 sortAnnByLabel.addActionListener(new ActionListener()
673 public void actionPerformed(ActionEvent e)
675 boolean newState = sortAnnByLabel.getState();
676 sortAnnBySequence.setSelected(false);
677 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
678 : SequenceAnnotationOrder.NONE);
679 sortAnnotations_actionPerformed();
682 colourTextMenuItem = new JCheckBoxMenuItem(
684 .getString("label.colour_text"));
685 colourTextMenuItem.addActionListener(new ActionListener()
688 public void actionPerformed(ActionEvent e)
690 colourTextMenuItem_actionPerformed(e);
694 JMenuItem htmlMenuItem = new JMenuItem(
695 MessageManager.getString("label.html"));
696 htmlMenuItem.addActionListener(new ActionListener()
699 public void actionPerformed(ActionEvent e)
701 htmlMenuItem_actionPerformed(e);
705 JMenuItem createBioJS = new JMenuItem(
706 MessageManager.getString("label.biojs_html_export"));
707 createBioJS.addActionListener(new java.awt.event.ActionListener()
710 public void actionPerformed(ActionEvent e)
712 bioJSMenuItem_actionPerformed(e);
716 JMenuItem overviewMenuItem = new JMenuItem(
717 MessageManager.getString("label.overview_window"));
718 overviewMenuItem.addActionListener(new ActionListener()
721 public void actionPerformed(ActionEvent e)
723 overviewMenuItem_actionPerformed(e);
727 undoMenuItem.setEnabled(false);
728 undoMenuItem.setText(MessageManager.getString("action.undo"));
729 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
730 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
731 al = new ActionListener()
734 public void actionPerformed(ActionEvent e)
736 undoMenuItem_actionPerformed(e);
739 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
741 redoMenuItem.setEnabled(false);
742 redoMenuItem.setText(MessageManager.getString("action.redo"));
743 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
744 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
745 al = new ActionListener()
748 public void actionPerformed(ActionEvent e)
750 redoMenuItem_actionPerformed(e);
753 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
755 conservationMenuItem.setText(MessageManager
756 .getString("action.by_conservation"));
757 conservationMenuItem.addActionListener(new ActionListener()
760 public void actionPerformed(ActionEvent e)
762 conservationMenuItem_actionPerformed();
766 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
767 wrapMenuItem.addActionListener(new ActionListener()
770 public void actionPerformed(ActionEvent e)
772 wrapMenuItem_actionPerformed(e);
776 JMenuItem printMenuItem = new JMenuItem(
777 MessageManager.getString("action.print"));
778 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
779 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
780 al = new ActionListener()
783 public void actionPerformed(ActionEvent e)
785 printMenuItem_actionPerformed(e);
788 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
791 .setText(MessageManager.getString("action.show_gaps"));
792 renderGapsMenuItem.setState(true);
793 renderGapsMenuItem.addActionListener(new ActionListener()
796 public void actionPerformed(ActionEvent e)
798 renderGapsMenuItem_actionPerformed(e);
802 JMenuItem findMenuItem = new JMenuItem(
803 MessageManager.getString("action.find"));
804 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
805 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
806 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
807 MessageManager.getString("label.find_tip")));
808 al = new ActionListener()
811 public void actionPerformed(ActionEvent e)
813 findMenuItem_actionPerformed(e);
816 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
818 abovePIDThreshold.setText(MessageManager
819 .getString("label.above_identity_threshold"));
820 abovePIDThreshold.addActionListener(new ActionListener()
823 public void actionPerformed(ActionEvent e)
825 abovePIDThreshold_actionPerformed();
829 showSeqFeatures.setText(MessageManager
830 .getString("label.show_sequence_features"));
831 showSeqFeatures.addActionListener(new ActionListener()
834 public void actionPerformed(ActionEvent actionEvent)
836 showSeqFeatures_actionPerformed(actionEvent);
840 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
841 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
842 * void actionPerformed(ActionEvent actionEvent) {
843 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
845 showDbRefsMenuitem.setText(MessageManager
846 .getString("label.show_database_refs"));
847 showDbRefsMenuitem.addActionListener(new ActionListener()
851 public void actionPerformed(ActionEvent e)
853 showDbRefs_actionPerformed(e);
857 showNpFeatsMenuitem.setText(MessageManager
858 .getString("label.show_non_positional_features"));
859 showNpFeatsMenuitem.addActionListener(new ActionListener()
863 public void actionPerformed(ActionEvent e)
865 showNpFeats_actionPerformed(e);
869 showGroupConservation.setText(MessageManager
870 .getString("label.group_conservation"));
871 showGroupConservation.addActionListener(new ActionListener()
875 public void actionPerformed(ActionEvent e)
877 showGroupConservation_actionPerformed(e);
882 showGroupConsensus.setText(MessageManager
883 .getString("label.group_consensus"));
884 showGroupConsensus.addActionListener(new ActionListener()
888 public void actionPerformed(ActionEvent e)
890 showGroupConsensus_actionPerformed(e);
894 showConsensusHistogram.setText(MessageManager
895 .getString("label.show_consensus_histogram"));
896 showConsensusHistogram.addActionListener(new ActionListener()
900 public void actionPerformed(ActionEvent e)
902 showConsensusHistogram_actionPerformed(e);
906 showSequenceLogo.setText(MessageManager
907 .getString("label.show_consensus_logo"));
908 showSequenceLogo.addActionListener(new ActionListener()
912 public void actionPerformed(ActionEvent e)
914 showSequenceLogo_actionPerformed(e);
918 normaliseSequenceLogo.setText(MessageManager
919 .getString("label.norm_consensus_logo"));
920 normaliseSequenceLogo.addActionListener(new ActionListener()
924 public void actionPerformed(ActionEvent e)
926 normaliseSequenceLogo_actionPerformed(e);
930 applyAutoAnnotationSettings.setText(MessageManager
931 .getString("label.apply_all_groups"));
932 applyAutoAnnotationSettings.setState(false);
933 applyAutoAnnotationSettings.setVisible(true);
934 applyAutoAnnotationSettings.addActionListener(new ActionListener()
937 public void actionPerformed(ActionEvent e)
939 applyAutoAnnotationSettings_actionPerformed(e);
943 ButtonGroup buttonGroup = new ButtonGroup();
944 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
945 MessageManager.getString("label.show_first"));
946 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
947 MessageManager.getString("label.show_last"));
948 buttonGroup.add(showAutoFirst);
949 buttonGroup.add(showAutoLast);
950 final boolean autoFirst = Cache.getDefault(
951 Preferences.SHOW_AUTOCALC_ABOVE, false);
952 showAutoFirst.setSelected(autoFirst);
953 setShowAutoCalculatedAbove(autoFirst);
954 showAutoFirst.addActionListener(new ActionListener()
957 public void actionPerformed(ActionEvent e)
959 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
960 sortAnnotations_actionPerformed();
963 showAutoLast.setSelected(!showAutoFirst.isSelected());
964 showAutoLast.addActionListener(new ActionListener()
967 public void actionPerformed(ActionEvent e)
969 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
970 sortAnnotations_actionPerformed();
974 JMenuItem deleteGroups = new JMenuItem(
975 MessageManager.getString("action.undefine_groups"));
976 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
977 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
978 al = new ActionListener()
981 public void actionPerformed(ActionEvent e)
983 deleteGroups_actionPerformed(e);
986 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
988 JMenuItem annotationColumn = new JMenuItem(
989 MessageManager.getString("action.select_by_annotation"));
990 annotationColumn.addActionListener(new ActionListener()
993 public void actionPerformed(ActionEvent e)
995 annotationColumn_actionPerformed(e);
999 JMenuItem createGroup = new JMenuItem(
1000 MessageManager.getString("action.create_groups"));
1001 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1002 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1003 al = new ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 createGroup_actionPerformed(e);
1011 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1013 JMenuItem unGroup = new JMenuItem(
1014 MessageManager.getString("action.remove_group"));
1015 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1016 .getDefaultToolkit().getMenuShortcutKeyMask()
1017 | KeyEvent.SHIFT_MASK, false);
1018 al = new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 unGroup_actionPerformed(e);
1026 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1028 copy.setText(MessageManager.getString("action.copy"));
1029 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1030 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1032 al = new ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 copy_actionPerformed(e);
1040 addMenuActionAndAccelerator(keyStroke, copy, al);
1042 cut.setText(MessageManager.getString("action.cut"));
1043 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1044 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1045 al = new ActionListener()
1048 public void actionPerformed(ActionEvent e)
1050 cut_actionPerformed(e);
1053 addMenuActionAndAccelerator(keyStroke, cut, al);
1055 JMenuItem delete = new JMenuItem(
1056 MessageManager.getString("action.delete"));
1057 delete.addActionListener(new ActionListener()
1060 public void actionPerformed(ActionEvent e)
1062 delete_actionPerformed(e);
1066 pasteMenu.setText(MessageManager.getString("action.paste"));
1067 JMenuItem pasteNew = new JMenuItem(
1068 MessageManager.getString("label.to_new_alignment"));
1069 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1070 .getDefaultToolkit().getMenuShortcutKeyMask()
1071 | KeyEvent.SHIFT_MASK, false);
1072 al = new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 pasteNew_actionPerformed(e);
1080 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1082 JMenuItem pasteThis = new JMenuItem(
1083 MessageManager.getString("label.to_this_alignment"));
1084 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1085 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1086 al = new ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 pasteThis_actionPerformed(e);
1094 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1096 JMenuItem createPNG = new JMenuItem("PNG");
1097 createPNG.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1105 createPNG.setActionCommand(MessageManager
1106 .getString("label.save_png_image"));
1108 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1109 font.addActionListener(new ActionListener()
1112 public void actionPerformed(ActionEvent e)
1114 font_actionPerformed(e);
1117 seqLimits.setText(MessageManager
1118 .getString("label.show_sequence_limits"));
1119 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1120 seqLimits.addActionListener(new ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 seqLimit_actionPerformed(e);
1128 JMenuItem epsFile = new JMenuItem("EPS");
1129 epsFile.addActionListener(new ActionListener()
1132 public void actionPerformed(ActionEvent e)
1138 JMenuItem createSVG = new JMenuItem("SVG");
1139 createSVG.addActionListener(new ActionListener()
1142 public void actionPerformed(ActionEvent e)
1148 JMenuItem loadTreeMenuItem = new JMenuItem(
1149 MessageManager.getString("label.load_associated_tree"));
1150 loadTreeMenuItem.setActionCommand(MessageManager
1151 .getString("label.load_tree_for_sequence_set"));
1152 loadTreeMenuItem.addActionListener(new ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 loadTreeMenuItem_actionPerformed(e);
1161 scaleAbove.setVisible(false);
1162 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1163 scaleAbove.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 scaleAbove_actionPerformed(e);
1171 scaleLeft.setVisible(false);
1172 scaleLeft.setSelected(true);
1173 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1174 scaleLeft.addActionListener(new ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 scaleLeft_actionPerformed(e);
1182 scaleRight.setVisible(false);
1183 scaleRight.setSelected(true);
1184 scaleRight.setText(MessageManager.getString("action.scale_right"));
1185 scaleRight.addActionListener(new ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 scaleRight_actionPerformed(e);
1193 centreColumnLabelsMenuItem.setVisible(true);
1194 centreColumnLabelsMenuItem.setState(false);
1195 centreColumnLabelsMenuItem.setText(MessageManager
1196 .getString("label.centre_column_labels"));
1197 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1200 public void actionPerformed(ActionEvent e)
1202 centreColumnLabels_actionPerformed(e);
1205 followHighlightMenuItem.setVisible(true);
1206 followHighlightMenuItem.setState(true);
1207 followHighlightMenuItem.setText(MessageManager
1208 .getString("label.automatic_scrolling"));
1209 followHighlightMenuItem.addActionListener(new ActionListener()
1213 public void actionPerformed(ActionEvent e)
1215 followHighlight_actionPerformed();
1220 modifyPID = new JMenuItem(
1221 MessageManager.getString("label.modify_identity_threshold"));
1222 modifyPID.addActionListener(new ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 modifyPID_actionPerformed();
1230 modifyConservation.setText(MessageManager
1231 .getString("label.modify_conservation_threshold"));
1232 modifyConservation.addActionListener(new ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 modifyConservation_actionPerformed();
1242 .setText(MessageManager.getString("action.by_tree_order"));
1243 sort.setText(MessageManager.getString("action.sort"));
1244 sort.addMenuListener(new MenuListener()
1247 public void menuSelected(MenuEvent e)
1253 public void menuDeselected(MenuEvent e)
1258 public void menuCanceled(MenuEvent e)
1262 sortByAnnotScore.setText(MessageManager
1263 .getString("label.sort_by_score"));
1264 sort.add(sortByAnnotScore);
1265 sort.addMenuListener(new javax.swing.event.MenuListener()
1269 public void menuCanceled(MenuEvent e)
1274 public void menuDeselected(MenuEvent e)
1279 public void menuSelected(MenuEvent e)
1281 buildSortByAnnotationScoresMenu();
1284 sortByAnnotScore.setVisible(false);
1287 .setText(MessageManager.getString("action.calculate_tree"));
1289 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1290 padGapsMenuitem.setState(jalview.bin.Cache
1291 .getDefault("PAD_GAPS", false));
1292 padGapsMenuitem.addActionListener(new ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 padGapsMenuitem_actionPerformed(e);
1300 JMenuItem vamsasStore = new JMenuItem(
1301 MessageManager.getString("label.vamsas_store"));
1302 vamsasStore.setVisible(false);
1303 vamsasStore.addActionListener(new ActionListener()
1306 public void actionPerformed(ActionEvent e)
1308 vamsasStore_actionPerformed(e);
1311 showTranslation.setText(MessageManager
1312 .getString("label.translate_cDNA"));
1313 showTranslation.addActionListener(new ActionListener()
1316 public void actionPerformed(ActionEvent e)
1318 showTranslation_actionPerformed(e);
1321 showReverse.setText(MessageManager.getString("label.reverse"));
1322 showReverse.addActionListener(new ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 showReverse_actionPerformed(false);
1330 showReverseComplement.setText(MessageManager
1331 .getString("label.reverse_complement"));
1332 showReverseComplement.addActionListener(new ActionListener()
1335 public void actionPerformed(ActionEvent e)
1337 showReverse_actionPerformed(true);
1341 JMenuItem extractScores = new JMenuItem(
1342 MessageManager.getString("label.extract_scores"));
1343 extractScores.addActionListener(new ActionListener()
1346 public void actionPerformed(ActionEvent e)
1348 extractScores_actionPerformed(e);
1351 extractScores.setVisible(true);
1352 // JBPNote: TODO: make gui for regex based score extraction
1354 // for show products actions see AlignFrame.canShowProducts
1355 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1357 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1358 runGroovy.setToolTipText(MessageManager
1359 .getString("label.run_groovy_tip"));
1360 runGroovy.addActionListener(new ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 runGroovy_actionPerformed();
1369 JMenuItem openFeatureSettings = new JMenuItem(
1370 MessageManager.getString("action.feature_settings"));
1371 openFeatureSettings.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 featureSettings_actionPerformed(e);
1379 JMenuItem fetchSequence = new JMenuItem(
1380 MessageManager.getString("label.fetch_sequences"));
1381 fetchSequence.addActionListener(new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 fetchSequence_actionPerformed(e);
1390 JMenuItem associatedData = new JMenuItem(
1391 MessageManager.getString("label.load_features_annotations"));
1392 associatedData.addActionListener(new ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 associatedData_actionPerformed(e);
1400 autoCalculate.setText(MessageManager
1401 .getString("label.autocalculate_consensus"));
1402 autoCalculate.setState(jalview.bin.Cache.getDefault(
1403 "AUTO_CALC_CONSENSUS", true));
1404 autoCalculate.addActionListener(new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 autoCalculate_actionPerformed(e);
1412 sortByTree.setText(MessageManager
1413 .getString("label.sort_alignment_new_tree"));
1415 .setToolTipText("<html>"
1417 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1419 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1420 sortByTree.addActionListener(new ActionListener()
1423 public void actionPerformed(ActionEvent e)
1425 sortByTreeOption_actionPerformed(e);
1429 listenToViewSelections.setText(MessageManager
1430 .getString("label.listen_for_selections"));
1431 listenToViewSelections
1432 .setToolTipText("<html>"
1434 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1435 listenToViewSelections.setState(false);
1436 listenToViewSelections.addActionListener(new ActionListener()
1439 public void actionPerformed(ActionEvent e)
1441 listenToViewSelections_actionPerformed(e);
1445 JMenu addSequenceMenu = new JMenu(
1446 MessageManager.getString("label.add_sequences"));
1447 JMenuItem addFromFile = new JMenuItem(
1448 MessageManager.getString("label.from_file"));
1449 addFromFile.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 addFromFile_actionPerformed(e);
1457 JMenuItem addFromText = new JMenuItem(
1458 MessageManager.getString("label.from_textbox"));
1459 addFromText.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 addFromText_actionPerformed(e);
1467 JMenuItem addFromURL = new JMenuItem(
1468 MessageManager.getString("label.from_url"));
1469 addFromURL.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 addFromURL_actionPerformed(e);
1477 JMenuItem exportFeatures = new JMenuItem(
1478 MessageManager.getString("label.export_features"));
1479 exportFeatures.addActionListener(new ActionListener()
1482 public void actionPerformed(ActionEvent e)
1484 exportFeatures_actionPerformed(e);
1487 JMenuItem exportAnnotations = new JMenuItem(
1488 MessageManager.getString("label.export_annotations"));
1489 exportAnnotations.addActionListener(new ActionListener()
1492 public void actionPerformed(ActionEvent e)
1494 exportAnnotations_actionPerformed(e);
1497 statusPanel.setLayout(new GridLayout());
1498 JMenuItem showAllSeqs = new JMenuItem(
1499 MessageManager.getString("label.all_sequences"));
1500 showAllSeqs.setToolTipText(MessageManager
1501 .getString("label.toggle_sequence_visibility"));
1502 showAllSeqs.addActionListener(new ActionListener()
1505 public void actionPerformed(ActionEvent e)
1507 showAllSeqs_actionPerformed(e);
1510 JMenuItem showAllColumns = new JMenuItem(
1511 MessageManager.getString("label.all_columns"));
1512 showAllColumns.setToolTipText(MessageManager
1513 .getString("label.toggle_columns_visibility"));
1514 showAllColumns.addActionListener(new ActionListener()
1517 public void actionPerformed(ActionEvent e)
1519 showAllColumns_actionPerformed(e);
1522 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1523 JMenuItem hideSelSequences = new JMenuItem(
1524 MessageManager.getString("label.selected_sequences"));
1525 hideSelSequences.setToolTipText(MessageManager
1526 .getString("label.toggle_sequence_visibility"));
1527 hideSelSequences.addActionListener(new ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 hideSelSequences_actionPerformed(e);
1535 JMenuItem hideSelColumns = new JMenuItem(
1536 MessageManager.getString("label.selected_columns"));
1537 hideSelColumns.setToolTipText(MessageManager
1538 .getString("label.toggle_columns_visibility"));
1539 hideSelColumns.addActionListener(new ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 hideSelColumns_actionPerformed(e);
1547 JMenuItem hideAllSelection = new JMenuItem(
1548 MessageManager.getString("label.selected_region"));
1549 hideAllSelection.addActionListener(new ActionListener()
1552 public void actionPerformed(ActionEvent e)
1554 hideAllSelection_actionPerformed(e);
1557 // TODO: should be hidden if no selection exists.
1558 JMenuItem hideAllButSelection = new JMenuItem(
1559 MessageManager.getString("label.all_but_selected_region"));
1560 hideAllButSelection.addActionListener(new ActionListener()
1563 public void actionPerformed(ActionEvent e)
1565 hideAllButSelection_actionPerformed(e);
1568 JMenuItem showAllhidden = new JMenuItem(
1569 MessageManager.getString("label.all_sequences_columns"));
1570 showAllhidden.setToolTipText(MessageManager
1571 .getString("label.toggles_visibility_hidden_selected_regions"));
1572 showAllhidden.addActionListener(new ActionListener()
1575 public void actionPerformed(ActionEvent e)
1577 showAllhidden_actionPerformed(e);
1580 hiddenMarkers.setText(MessageManager
1581 .getString("action.show_hidden_markers"));
1582 hiddenMarkers.addActionListener(new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 hiddenMarkers_actionPerformed(e);
1591 JMenuItem invertColSel = new JMenuItem(
1592 MessageManager.getString("action.invert_column_selection"));
1593 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1594 .getDefaultToolkit().getMenuShortcutKeyMask()
1595 | KeyEvent.ALT_MASK, false);
1596 al = new ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 invertColSel_actionPerformed(e);
1604 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1606 showComplementMenuItem.setVisible(false);
1607 showComplementMenuItem.addActionListener(new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 showComplement_actionPerformed(showComplementMenuItem.getState());
1616 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1619 public void stateChanged(ChangeEvent evt)
1621 JTabbedPane pane = (JTabbedPane) evt.getSource();
1622 int sel = pane.getSelectedIndex();
1623 tabSelectionChanged(sel);
1626 tabbedPane.addMouseListener(new MouseAdapter()
1629 public void mousePressed(MouseEvent e)
1631 if (e.isPopupTrigger()) // Mac
1633 tabbedPane_mousePressed(e);
1638 public void mouseReleased(MouseEvent e)
1640 if (e.isPopupTrigger()) // Windows
1642 tabbedPane_mousePressed(e);
1646 tabbedPane.addFocusListener(new FocusAdapter()
1649 public void focusGained(FocusEvent e)
1651 tabbedPane_focusGained(e);
1655 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1656 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1657 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1658 al = new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 save_actionPerformed(e);
1666 addMenuActionAndAccelerator(keyStroke, save, al);
1668 reload.setEnabled(false);
1669 reload.setText(MessageManager.getString("action.reload"));
1670 reload.addActionListener(new ActionListener()
1673 public void actionPerformed(ActionEvent e)
1675 reload_actionPerformed(e);
1679 JMenuItem newView = new JMenuItem(
1680 MessageManager.getString("action.new_view"));
1681 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1682 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1683 al = new ActionListener()
1686 public void actionPerformed(ActionEvent e)
1688 newView_actionPerformed(e);
1691 addMenuActionAndAccelerator(keyStroke, newView, al);
1693 tabbedPane.setToolTipText("<html><i>"
1694 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1697 formatMenu.setText(MessageManager.getString("action.format"));
1698 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1699 idRightAlign.setText(MessageManager
1700 .getString("label.right_align_sequence_id"));
1701 idRightAlign.addActionListener(new ActionListener()
1704 public void actionPerformed(ActionEvent e)
1706 idRightAlign_actionPerformed(e);
1710 gatherViews.setEnabled(false);
1711 gatherViews.setText(MessageManager.getString("action.gather_views"));
1712 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1713 al = new ActionListener()
1716 public void actionPerformed(ActionEvent e)
1718 gatherViews_actionPerformed(e);
1721 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1723 expandViews.setEnabled(false);
1724 expandViews.setText(MessageManager.getString("action.expand_views"));
1725 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1726 al = new ActionListener()
1729 public void actionPerformed(ActionEvent e)
1731 expandViews_actionPerformed(e);
1734 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1736 JMenuItem pageSetup = new JMenuItem(
1737 MessageManager.getString("action.page_setup"));
1738 pageSetup.addActionListener(new ActionListener()
1741 public void actionPerformed(ActionEvent e)
1743 pageSetup_actionPerformed(e);
1746 JMenuItem alignmentProperties = new JMenuItem(
1747 MessageManager.getString("label.alignment_props"));
1748 alignmentProperties.addActionListener(new ActionListener()
1751 public void actionPerformed(ActionEvent actionEvent)
1753 alignmentProperties();
1756 JMenuItem selectHighlighted = new JMenuItem(
1757 MessageManager.getString("action.select_highlighted_columns"));
1758 selectHighlighted.setToolTipText(MessageManager
1759 .getString("tooltip.select_highlighted_columns"));
1760 al = new ActionListener()
1763 public void actionPerformed(ActionEvent actionEvent)
1765 selectHighlightedColumns_actionPerformed(actionEvent);
1768 selectHighlighted.addActionListener(al);
1769 JMenu tooltipSettingsMenu = new JMenu(
1770 MessageManager.getString("label.sequence_id_tooltip"));
1771 JMenu autoAnnMenu = new JMenu(
1772 MessageManager.getString("label.autocalculated_annotation"));
1774 JMenu exportImageMenu = new JMenu(
1775 MessageManager.getString("label.export_image"));
1776 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1777 alignFrameMenuBar.add(fileMenu);
1778 alignFrameMenuBar.add(editMenu);
1779 alignFrameMenuBar.add(selectMenu);
1780 alignFrameMenuBar.add(viewMenu);
1781 alignFrameMenuBar.add(annotationsMenu);
1782 alignFrameMenuBar.add(formatMenu);
1783 alignFrameMenuBar.add(colourMenu);
1784 alignFrameMenuBar.add(calculateMenu);
1785 alignFrameMenuBar.add(webService);
1787 fileMenu.add(fetchSequence);
1788 fileMenu.add(addSequenceMenu);
1789 fileMenu.add(reload);
1790 fileMenu.addSeparator();
1791 fileMenu.add(vamsasStore);
1793 fileMenu.add(saveAs);
1794 fileMenu.add(outputTextboxMenu);
1795 fileMenu.add(pageSetup);
1796 fileMenu.add(printMenuItem);
1797 fileMenu.addSeparator();
1798 fileMenu.add(exportImageMenu);
1799 fileMenu.add(exportFeatures);
1800 fileMenu.add(exportAnnotations);
1801 fileMenu.add(loadTreeMenuItem);
1802 fileMenu.add(associatedData);
1803 fileMenu.addSeparator();
1804 fileMenu.add(closeMenuItem);
1806 pasteMenu.add(pasteNew);
1807 pasteMenu.add(pasteThis);
1808 editMenu.add(undoMenuItem);
1809 editMenu.add(redoMenuItem);
1812 editMenu.add(pasteMenu);
1813 editMenu.add(delete);
1814 editMenu.addSeparator();
1815 editMenu.add(remove2LeftMenuItem);
1816 editMenu.add(remove2RightMenuItem);
1817 editMenu.add(removeGappedColumnMenuItem);
1818 editMenu.add(removeAllGapsMenuItem);
1819 editMenu.add(removeRedundancyMenuItem);
1820 editMenu.addSeparator();
1821 // dont add these yet in the CVS build - they cannot be undone!
1822 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1823 // editMenu.add(justifyLeftMenuItem);
1824 // editMenu.add(justifyRightMenuItem);
1825 // editMenu.addSeparator();
1826 editMenu.add(padGapsMenuitem);
1828 showMenu.add(showAllColumns);
1829 showMenu.add(showAllSeqs);
1830 showMenu.add(showAllhidden);
1831 hideMenu.add(hideSelColumns);
1832 hideMenu.add(hideSelSequences);
1833 hideMenu.add(hideAllSelection);
1834 hideMenu.add(hideAllButSelection);
1835 viewMenu.add(newView);
1836 viewMenu.add(expandViews);
1837 viewMenu.add(gatherViews);
1838 viewMenu.addSeparator();
1839 viewMenu.add(showMenu);
1840 viewMenu.add(hideMenu);
1841 viewMenu.add(showComplementMenuItem);
1842 viewMenu.addSeparator();
1843 viewMenu.add(followHighlightMenuItem);
1844 viewMenu.addSeparator();
1845 viewMenu.add(showSeqFeatures);
1846 // viewMenu.add(showSeqFeaturesHeight);
1847 viewMenu.add(openFeatureSettings);
1848 tooltipSettingsMenu.add(showDbRefsMenuitem);
1849 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1850 viewMenu.add(tooltipSettingsMenu);
1851 viewMenu.addSeparator();
1852 viewMenu.add(alignmentProperties);
1853 viewMenu.addSeparator();
1854 viewMenu.add(overviewMenuItem);
1856 annotationsMenu.add(annotationPanelMenuItem);
1857 annotationsMenu.addSeparator();
1858 annotationsMenu.add(showAllAlAnnotations);
1859 annotationsMenu.add(hideAllAlAnnotations);
1860 annotationsMenu.addSeparator();
1861 annotationsMenu.add(showAllSeqAnnotations);
1862 annotationsMenu.add(hideAllSeqAnnotations);
1863 annotationsMenu.add(sortAnnBySequence);
1864 annotationsMenu.add(sortAnnByLabel);
1865 annotationsMenu.addSeparator();
1866 autoAnnMenu.add(showAutoFirst);
1867 autoAnnMenu.add(showAutoLast);
1868 autoAnnMenu.addSeparator();
1869 autoAnnMenu.add(applyAutoAnnotationSettings);
1870 autoAnnMenu.add(showConsensusHistogram);
1871 autoAnnMenu.add(showSequenceLogo);
1872 autoAnnMenu.add(normaliseSequenceLogo);
1873 autoAnnMenu.addSeparator();
1874 autoAnnMenu.add(showGroupConservation);
1875 autoAnnMenu.add(showGroupConsensus);
1876 annotationsMenu.add(autoAnnMenu);
1879 sort.add(sortIDMenuItem);
1880 sort.add(sortLengthMenuItem);
1881 sort.add(sortGroupMenuItem);
1882 sort.add(sortPairwiseMenuItem);
1883 sort.add(sortByTreeMenu);
1884 calculateMenu.add(sort);
1885 calculateMenu.add(calculateTree);
1886 calculateMenu.addSeparator();
1887 calculateMenu.add(pairwiseAlignmentMenuItem);
1888 calculateMenu.add(PCAMenuItem);
1889 calculateMenu.addSeparator();
1890 calculateMenu.add(showTranslation);
1891 calculateMenu.add(showReverse);
1892 calculateMenu.add(showReverseComplement);
1893 calculateMenu.add(showProducts);
1894 calculateMenu.add(autoCalculate);
1895 calculateMenu.add(sortByTree);
1896 calculateMenu.addSeparator();
1897 calculateMenu.add(expandAlignment);
1898 calculateMenu.add(extractScores);
1899 calculateMenu.addSeparator();
1900 calculateMenu.add(runGroovy);
1902 webServiceNoServices = new JMenuItem(
1903 MessageManager.getString("label.no_services"));
1904 webService.add(webServiceNoServices);
1905 exportImageMenu.add(htmlMenuItem);
1906 exportImageMenu.add(epsFile);
1907 exportImageMenu.add(createPNG);
1908 exportImageMenu.add(createBioJS);
1909 exportImageMenu.add(createSVG);
1910 addSequenceMenu.add(addFromFile);
1911 addSequenceMenu.add(addFromText);
1912 addSequenceMenu.add(addFromURL);
1913 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1914 statusPanel.add(statusBar, null);
1915 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1917 formatMenu.add(font);
1918 formatMenu.addSeparator();
1919 formatMenu.add(wrapMenuItem);
1920 formatMenu.add(scaleAbove);
1921 formatMenu.add(scaleLeft);
1922 formatMenu.add(scaleRight);
1923 formatMenu.add(seqLimits);
1924 formatMenu.add(idRightAlign);
1925 formatMenu.add(hiddenMarkers);
1926 formatMenu.add(viewBoxesMenuItem);
1927 formatMenu.add(viewTextMenuItem);
1928 formatMenu.add(colourTextMenuItem);
1929 formatMenu.add(renderGapsMenuItem);
1930 formatMenu.add(centreColumnLabelsMenuItem);
1931 formatMenu.add(showNonconservedMenuItem);
1932 selectMenu.add(findMenuItem);
1933 selectMenu.addSeparator();
1934 selectMenu.add(selectAllSequenceMenuItem);
1935 selectMenu.add(deselectAllSequenceMenuItem);
1936 selectMenu.add(invertSequenceMenuItem);
1937 selectMenu.add(invertColSel);
1938 selectMenu.add(createGroup);
1939 selectMenu.add(unGroup);
1940 selectMenu.add(grpsFromSelection);
1941 selectMenu.add(deleteGroups);
1942 selectMenu.add(annotationColumn);
1943 selectMenu.add(selectHighlighted);
1944 // TODO - determine if the listenToViewSelections button is needed : see bug
1946 // selectMenu.addSeparator();
1947 // selectMenu.add(listenToViewSelections);
1951 * Constructs the entries on the Colour menu (but does not add them to the
1954 protected void initColourMenu()
1956 applyToAllGroups = new JCheckBoxMenuItem(
1957 MessageManager.getString("label.apply_colour_to_all_groups"));
1958 applyToAllGroups.addActionListener(new ActionListener()
1961 public void actionPerformed(ActionEvent e)
1963 applyToAllGroups_actionPerformed();
1967 textColour = new JRadioButtonMenuItem(
1968 MessageManager.getString("action.set_text_colour"));
1969 textColour.addActionListener(new ActionListener()
1972 public void actionPerformed(ActionEvent e)
1974 textColour_actionPerformed();
1978 conservationMenuItem = new JCheckBoxMenuItem(
1979 MessageManager.getString("action.by_conservation"));
1980 conservationMenuItem.addActionListener(new ActionListener()
1983 public void actionPerformed(ActionEvent e)
1985 conservationMenuItem_actionPerformed();
1989 abovePIDThreshold = new JCheckBoxMenuItem(
1990 MessageManager.getString("label.above_identity_threshold"));
1991 abovePIDThreshold.addActionListener(new ActionListener()
1994 public void actionPerformed(ActionEvent e)
1996 abovePIDThreshold_actionPerformed();
1999 modifyPID = new JMenuItem(
2000 MessageManager.getString("label.modify_identity_threshold"));
2001 modifyPID.addActionListener(new ActionListener()
2004 public void actionPerformed(ActionEvent e)
2006 modifyPID_actionPerformed();
2009 modifyConservation = new JMenuItem(
2011 .getString("label.modify_conservation_threshold"));
2012 modifyConservation.addActionListener(new ActionListener()
2015 public void actionPerformed(ActionEvent e)
2017 modifyConservation_actionPerformed();
2021 annotationColour = new JMenuItem(
2022 MessageManager.getString("action.by_annotation"));
2023 annotationColour.addActionListener(new ActionListener()
2026 public void actionPerformed(ActionEvent e)
2028 annotationColour_actionPerformed();
2033 protected void selectHighlightedColumns_actionPerformed(
2034 ActionEvent actionEvent)
2036 // TODO Auto-generated method stub
2041 * Generate the reverse sequence (or reverse complement if the flag is true)
2042 * and add it to the alignment
2046 protected void showReverse_actionPerformed(boolean complement)
2051 * Try to run script in a Groovy console, having first ensured that this
2052 * alignframe is set as currentAlignFrame in Desktop
2054 protected void runGroovy_actionPerformed()
2060 * Adds the given action listener and key accelerator to the given menu item.
2061 * Also saves in a lookup table to support lookup of action by key stroke.
2065 * @param actionListener
2067 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2068 JMenuItem menuItem, ActionListener actionListener)
2070 menuItem.setAccelerator(keyStroke);
2071 accelerators.put(keyStroke, menuItem);
2072 menuItem.addActionListener(actionListener);
2076 * Action on clicking sort annotations by type.
2080 protected void sortAnnotations_actionPerformed()
2085 * Action on clicking Show all annotations.
2087 * @param forSequences
2088 * update sequence-related annotations
2089 * @param forAlignment
2090 * update non-sequence-related annotations
2092 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2093 boolean forAlignment)
2095 setAnnotationsVisibility(true, forSequences, forAlignment);
2099 * Action on clicking Hide all annotations.
2101 * @param forSequences
2102 * update sequence-related annotations
2103 * @param forAlignment
2104 * update non-sequence-related annotations
2106 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2107 boolean forAlignment)
2109 setAnnotationsVisibility(false, forSequences, forAlignment);
2113 * Set the visibility of annotations to true or false. Can act on
2114 * sequence-related annotations, or alignment-related, or both.
2117 * @param forSequences
2118 * update sequence-related annotations
2119 * @param forAlignment
2120 * update non-sequence-related annotations
2122 protected void setAnnotationsVisibility(boolean visible,
2123 boolean forSequences, boolean forAlignment)
2128 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2130 // TODO Auto-generated method stub
2134 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2136 // TODO Auto-generated method stub
2140 protected void showAllhidden_actionPerformed(ActionEvent e)
2142 // TODO Auto-generated method stub
2146 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2148 // TODO Auto-generated method stub
2152 protected void hideAllSelection_actionPerformed(ActionEvent e)
2154 // TODO Auto-generated method stub
2158 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2160 // TODO Auto-generated method stub
2164 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2166 // TODO Auto-generated method stub
2170 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2172 // TODO Auto-generated method stub
2176 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2178 // TODO Auto-generated method stub
2182 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2184 // TODO Auto-generated method stub
2188 protected void showGroupConservation_actionPerformed(ActionEvent e)
2190 // TODO Auto-generated method stub
2194 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2196 // TODO Auto-generated method stub
2200 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2202 // TODO Auto-generated method stub
2206 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2208 // TODO Auto-generated method stub
2212 protected void followHighlight_actionPerformed()
2214 // TODO Auto-generated method stub
2218 protected void showNpFeats_actionPerformed(ActionEvent e)
2220 // TODO Auto-generated method stub
2224 protected void showDbRefs_actionPerformed(ActionEvent e)
2226 // TODO Auto-generated method stub
2230 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2234 protected void buildSortByAnnotationScoresMenu()
2238 protected void extractScores_actionPerformed(ActionEvent e)
2242 protected void outputText_actionPerformed(ActionEvent e)
2246 public void addFromFile_actionPerformed(ActionEvent e)
2251 public void addFromText_actionPerformed(ActionEvent e)
2256 public void addFromURL_actionPerformed(ActionEvent e)
2261 public void exportFeatures_actionPerformed(ActionEvent e)
2266 public void exportAnnotations_actionPerformed(ActionEvent e)
2271 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2275 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2280 protected void closeMenuItem_actionPerformed(boolean b)
2284 protected void redoMenuItem_actionPerformed(ActionEvent e)
2288 protected void undoMenuItem_actionPerformed(ActionEvent e)
2292 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2296 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2300 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2304 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2308 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2312 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2316 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2320 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2324 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2328 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2332 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2336 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2340 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2344 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2348 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2352 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2356 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2360 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2364 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2368 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2372 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2376 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2380 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2384 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2388 protected void conservationMenuItem_actionPerformed()
2392 protected void printMenuItem_actionPerformed(ActionEvent e)
2396 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2400 protected void findMenuItem_actionPerformed(ActionEvent e)
2404 protected void abovePIDThreshold_actionPerformed()
2408 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2412 protected void deleteGroups_actionPerformed(ActionEvent e)
2416 protected void createGroup_actionPerformed(ActionEvent e)
2420 protected void unGroup_actionPerformed(ActionEvent e)
2424 protected void copy_actionPerformed(ActionEvent e)
2428 protected void cut_actionPerformed(ActionEvent e)
2432 protected void delete_actionPerformed(ActionEvent e)
2436 protected void pasteNew_actionPerformed(ActionEvent e)
2440 protected void pasteThis_actionPerformed(ActionEvent e)
2444 protected void applyToAllGroups_actionPerformed()
2448 public void createPNG(java.io.File f)
2452 protected void font_actionPerformed(ActionEvent e)
2456 protected void seqLimit_actionPerformed(ActionEvent e)
2460 public void seqDBRef_actionPerformed(ActionEvent e)
2465 public void createEPS(java.io.File f)
2469 public void createSVG(java.io.File f)
2474 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2480 * Template method to handle the 'load T-Coffee scores' menu event.
2482 * Subclasses override this method to provide a custom action.
2487 protected void loadScores_actionPerformed(ActionEvent event)
2492 protected void jpred_actionPerformed(ActionEvent e)
2496 protected void scaleAbove_actionPerformed(ActionEvent e)
2500 protected void scaleLeft_actionPerformed(ActionEvent e)
2504 protected void scaleRight_actionPerformed(ActionEvent e)
2508 protected void modifyPID_actionPerformed()
2512 protected void modifyConservation_actionPerformed()
2516 protected void saveAs_actionPerformed(ActionEvent e)
2520 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2524 public void vamsasStore_actionPerformed(ActionEvent e)
2529 public void vamsasLoad_actionPerformed(ActionEvent e)
2534 public void showTranslation_actionPerformed(ActionEvent e)
2539 public void featureSettings_actionPerformed(ActionEvent e)
2544 public void fetchSequence_actionPerformed(ActionEvent e)
2549 public void smoothFont_actionPerformed(ActionEvent e)
2554 public void annotationColour_actionPerformed()
2558 public void annotationColumn_actionPerformed(ActionEvent e)
2562 public void associatedData_actionPerformed(ActionEvent e)
2567 public void autoCalculate_actionPerformed(ActionEvent e)
2572 public void sortByTreeOption_actionPerformed(ActionEvent e)
2577 public void showAllSeqs_actionPerformed(ActionEvent e)
2582 public void showAllColumns_actionPerformed(ActionEvent e)
2587 public void hideSelSequences_actionPerformed(ActionEvent e)
2592 public void hideSelColumns_actionPerformed(ActionEvent e)
2597 public void hiddenMarkers_actionPerformed(ActionEvent e)
2602 public void findPdbId_actionPerformed(ActionEvent e)
2607 public void enterPdbId_actionPerformed(ActionEvent e)
2612 public void pdbFile_actionPerformed(ActionEvent e)
2617 public void invertColSel_actionPerformed(ActionEvent e)
2622 public void tabSelectionChanged(int sel)
2627 public void tabbedPane_mousePressed(MouseEvent e)
2632 public void tabbedPane_focusGained(FocusEvent e)
2637 public void save_actionPerformed(ActionEvent e)
2642 public void reload_actionPerformed(ActionEvent e)
2647 public void newView_actionPerformed(ActionEvent e)
2652 public void textColour_actionPerformed()
2657 public void idRightAlign_actionPerformed(ActionEvent e)
2662 public void expandViews_actionPerformed(ActionEvent e)
2667 public void gatherViews_actionPerformed(ActionEvent e)
2672 public void buildTreeMenu()
2677 public void pageSetup_actionPerformed(ActionEvent e)
2682 public void alignmentProperties()
2687 protected void expand_newalign(ActionEvent e)
2689 // TODO Auto-generated method stub
2693 protected boolean isShowAutoCalculatedAbove()
2695 return showAutoCalculatedAbove;
2698 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2700 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2703 protected SequenceAnnotationOrder getAnnotationSortOrder()
2705 return annotationSortOrder;
2708 protected void setAnnotationSortOrder(
2709 SequenceAnnotationOrder annotationSortOrder)
2711 this.annotationSortOrder = annotationSortOrder;
2714 public Map<KeyStroke, JMenuItem> getAccelerators()
2716 return this.accelerators;
2720 * Returns the selected index of the tabbed pane, or -1 if none selected
2721 * (including the case where the tabbed pane has not been made visible).
2725 public int getTabIndex()
2727 return tabbedPane.getSelectedIndex();
2730 public JPanel getStatusPanel()
2736 * Sets a reference to the containing split frame. Also makes the 'toggle
2737 * split view' menu item visible and checked.
2741 public void setSplitFrame(SplitContainerI sf)
2743 this.splitFrame = sf;
2746 this.showComplementMenuItem.setVisible(true);
2747 this.showComplementMenuItem.setState(true);
2751 public SplitContainerI getSplitViewContainer()
2753 return this.splitFrame;
2756 protected void showComplement_actionPerformed(boolean complement)