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;
206 protected JMenuItem createGroup;
208 protected JMenuItem unGroup;
215 setJMenuBar(alignFrameMenuBar);
217 // dynamically fill save as menu with available formats
218 for (String ff : FileFormats.getInstance().getWritableFormats(true))
220 JMenuItem item = new JMenuItem(ff);
222 item.addActionListener(new ActionListener()
225 public void actionPerformed(ActionEvent e)
227 outputText_actionPerformed(e);
231 outputTextboxMenu.add(item);
233 } catch (Exception e)
235 System.err.println(e.toString());
238 if (!Platform.isAMac())
240 closeMenuItem.setMnemonic('C');
241 outputTextboxMenu.setMnemonic('T');
242 undoMenuItem.setMnemonic('Z');
243 redoMenuItem.setMnemonic('0');
244 copy.setMnemonic('C');
245 cut.setMnemonic('U');
246 pasteMenu.setMnemonic('P');
247 reload.setMnemonic('R');
251 private void jbInit() throws Exception
255 JMenuItem saveAs = new JMenuItem(
256 MessageManager.getString("action.save_as"));
257 ActionListener al = new ActionListener()
260 public void actionPerformed(ActionEvent e)
262 saveAs_actionPerformed(e);
266 // FIXME getDefaultToolkit throws an exception in Headless mode
267 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
268 .getDefaultToolkit().getMenuShortcutKeyMask()
269 | KeyEvent.SHIFT_MASK, false);
270 addMenuActionAndAccelerator(keyStroke, saveAs, al);
272 closeMenuItem.setText(MessageManager.getString("action.close"));
273 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
274 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
275 al = new ActionListener()
278 public void actionPerformed(ActionEvent e)
280 closeMenuItem_actionPerformed(false);
283 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
285 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
286 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
287 JMenu annotationsMenu = new JMenu(
288 MessageManager.getString("action.annotations"));
289 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
290 colourMenu.setText(MessageManager.getString("action.colour"));
291 JMenu calculateMenu = new JMenu(
292 MessageManager.getString("action.calculate"));
293 webService.setText(MessageManager.getString("action.web_service"));
294 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
295 MessageManager.getString("action.select_all"));
296 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
297 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
298 al = new ActionListener()
301 public void actionPerformed(ActionEvent e)
303 selectAllSequenceMenuItem_actionPerformed(e);
306 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
308 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
309 MessageManager.getString("action.deselect_all"));
310 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
311 al = new ActionListener()
314 public void actionPerformed(ActionEvent e)
316 deselectAllSequenceMenuItem_actionPerformed(e);
319 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
321 JMenuItem invertSequenceMenuItem = new JMenuItem(
322 MessageManager.getString("action.invert_sequence_selection"));
323 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
324 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
325 al = new ActionListener()
328 public void actionPerformed(ActionEvent e)
330 invertSequenceMenuItem_actionPerformed(e);
333 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
335 JMenuItem grpsFromSelection = new JMenuItem(
336 MessageManager.getString("action.make_groups_selection"));
337 grpsFromSelection.addActionListener(new ActionListener()
340 public void actionPerformed(ActionEvent e)
342 makeGrpsFromSelection_actionPerformed(e);
345 JMenuItem expandAlignment = new JMenuItem(
346 MessageManager.getString("action.view_flanking_regions"));
347 expandAlignment.setToolTipText(MessageManager
348 .getString("label.view_flanking_regions"));
349 expandAlignment.addActionListener(new ActionListener()
352 public void actionPerformed(ActionEvent e)
357 JMenuItem remove2LeftMenuItem = new JMenuItem(
358 MessageManager.getString("action.remove_left"));
359 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
360 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
361 al = new ActionListener()
364 public void actionPerformed(ActionEvent e)
366 remove2LeftMenuItem_actionPerformed(e);
369 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
371 JMenuItem remove2RightMenuItem = new JMenuItem(
372 MessageManager.getString("action.remove_right"));
373 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
374 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
375 al = new ActionListener()
378 public void actionPerformed(ActionEvent e)
380 remove2RightMenuItem_actionPerformed(e);
383 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
385 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
386 MessageManager.getString("action.remove_empty_columns"));
387 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
388 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
389 al = new ActionListener()
392 public void actionPerformed(ActionEvent e)
394 removeGappedColumnMenuItem_actionPerformed(e);
397 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
399 JMenuItem removeAllGapsMenuItem = new JMenuItem(
400 MessageManager.getString("action.remove_all_gaps"));
401 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
402 .getDefaultToolkit().getMenuShortcutKeyMask()
403 | KeyEvent.SHIFT_MASK, false);
404 al = new ActionListener()
407 public void actionPerformed(ActionEvent e)
409 removeAllGapsMenuItem_actionPerformed(e);
412 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
414 JMenuItem justifyLeftMenuItem = new JMenuItem(
415 MessageManager.getString("action.left_justify_alignment"));
416 justifyLeftMenuItem.addActionListener(new ActionListener()
419 public void actionPerformed(ActionEvent e)
421 justifyLeftMenuItem_actionPerformed(e);
424 JMenuItem justifyRightMenuItem = new JMenuItem(
425 MessageManager.getString("action.right_justify_alignment"));
426 justifyRightMenuItem.addActionListener(new ActionListener()
429 public void actionPerformed(ActionEvent e)
431 justifyRightMenuItem_actionPerformed(e);
434 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
435 viewBoxesMenuItem.setState(true);
436 viewBoxesMenuItem.addActionListener(new ActionListener()
439 public void actionPerformed(ActionEvent e)
441 viewBoxesMenuItem_actionPerformed(e);
444 viewTextMenuItem.setText(MessageManager.getString("action.text"));
445 viewTextMenuItem.setState(true);
446 viewTextMenuItem.addActionListener(new ActionListener()
449 public void actionPerformed(ActionEvent e)
451 viewTextMenuItem_actionPerformed(e);
454 showNonconservedMenuItem.setText(MessageManager
455 .getString("label.show_non_conserved"));
456 showNonconservedMenuItem.setState(false);
457 showNonconservedMenuItem.addActionListener(new ActionListener()
460 public void actionPerformed(ActionEvent e)
462 showUnconservedMenuItem_actionPerformed(e);
465 JMenuItem sortPairwiseMenuItem = new JMenuItem(
466 MessageManager.getString("action.by_pairwise_id"));
467 sortPairwiseMenuItem.addActionListener(new ActionListener()
470 public void actionPerformed(ActionEvent e)
472 sortPairwiseMenuItem_actionPerformed(e);
475 JMenuItem sortIDMenuItem = new JMenuItem(
476 MessageManager.getString("action.by_id"));
477 sortIDMenuItem.addActionListener(new ActionListener()
480 public void actionPerformed(ActionEvent e)
482 sortIDMenuItem_actionPerformed(e);
485 JMenuItem sortLengthMenuItem = new JMenuItem(
486 MessageManager.getString("action.by_length"));
487 sortLengthMenuItem.addActionListener(new ActionListener()
490 public void actionPerformed(ActionEvent e)
492 sortLengthMenuItem_actionPerformed(e);
495 JMenuItem sortGroupMenuItem = new JMenuItem(
496 MessageManager.getString("action.by_group"));
497 sortGroupMenuItem.addActionListener(new ActionListener()
500 public void actionPerformed(ActionEvent e)
502 sortGroupMenuItem_actionPerformed(e);
506 JMenuItem removeRedundancyMenuItem = new JMenuItem(
507 MessageManager.getString("action.remove_redundancy"));
508 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
509 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
510 al = new ActionListener()
513 public void actionPerformed(ActionEvent e)
515 removeRedundancyMenuItem_actionPerformed(e);
518 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
520 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
521 MessageManager.getString("action.pairwise_alignment"));
522 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
525 public void actionPerformed(ActionEvent e)
527 pairwiseAlignmentMenuItem_actionPerformed(e);
530 JMenuItem PCAMenuItem = new JMenuItem(
531 MessageManager.getString("label.principal_component_analysis"));
532 PCAMenuItem.addActionListener(new ActionListener()
535 public void actionPerformed(ActionEvent e)
537 PCAMenuItem_actionPerformed(e);
540 JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
541 MessageManager.getString("label.average_distance_identity"));
542 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
545 public void actionPerformed(ActionEvent e)
547 averageDistanceTreeMenuItem_actionPerformed(e);
550 JMenuItem neighbourTreeMenuItem = new JMenuItem(
551 MessageManager.getString("label.neighbour_joining_identity"));
552 neighbourTreeMenuItem.addActionListener(new ActionListener()
555 public void actionPerformed(ActionEvent e)
557 neighbourTreeMenuItem_actionPerformed(e);
561 this.getContentPane().setLayout(new BorderLayout());
562 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
563 statusBar.setBackground(Color.white);
564 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
565 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
566 statusBar.setText(MessageManager.getString("label.status_bar"));
567 outputTextboxMenu.setText(MessageManager
568 .getString("label.out_to_textbox"));
571 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
572 MessageManager.getString("label.average_distance_blosum62"));
573 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
576 public void actionPerformed(ActionEvent e)
578 avTreeBlosumMenuItem_actionPerformed(e);
581 JMenuItem njTreeBlosumMenuItem = new JMenuItem(
582 MessageManager.getString("label.neighbour_blosum62"));
583 njTreeBlosumMenuItem.addActionListener(new ActionListener()
586 public void actionPerformed(ActionEvent e)
588 njTreeBlosumMenuItem_actionPerformed(e);
591 annotationPanelMenuItem.setActionCommand("");
592 annotationPanelMenuItem.setText(MessageManager
593 .getString("label.show_annotations"));
594 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
596 annotationPanelMenuItem.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent e)
601 annotationPanelMenuItem_actionPerformed(e);
604 showAllAlAnnotations.setText(MessageManager
605 .getString("label.show_all_al_annotations"));
606 final boolean isAnnotationPanelShown = annotationPanelMenuItem
608 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
609 showAllAlAnnotations.addActionListener(new ActionListener()
612 public void actionPerformed(ActionEvent e)
614 showAllAnnotations_actionPerformed(false, true);
617 hideAllAlAnnotations.setText(MessageManager
618 .getString("label.hide_all_al_annotations"));
619 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
620 hideAllAlAnnotations.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent e)
625 hideAllAnnotations_actionPerformed(false, true);
628 showAllSeqAnnotations.setText(MessageManager
629 .getString("label.show_all_seq_annotations"));
630 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
631 showAllSeqAnnotations.addActionListener(new ActionListener()
634 public void actionPerformed(ActionEvent e)
636 showAllAnnotations_actionPerformed(true, false);
639 hideAllSeqAnnotations.setText(MessageManager
640 .getString("label.hide_all_seq_annotations"));
641 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
642 hideAllSeqAnnotations.addActionListener(new ActionListener()
645 public void actionPerformed(ActionEvent e)
647 hideAllAnnotations_actionPerformed(true, false);
650 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
651 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
652 SequenceAnnotationOrder.NONE.name()));
653 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
654 MessageManager.getString("label.sort_annotations_by_sequence"));
655 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
656 MessageManager.getString("label.sort_annotations_by_label"));
659 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
660 sortAnnBySequence.addActionListener(new ActionListener()
663 public void actionPerformed(ActionEvent e)
665 boolean newState = sortAnnBySequence.getState();
666 sortAnnByLabel.setSelected(false);
667 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
668 : SequenceAnnotationOrder.NONE);
669 sortAnnotations_actionPerformed();
673 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
674 sortAnnByLabel.addActionListener(new ActionListener()
677 public void actionPerformed(ActionEvent e)
679 boolean newState = sortAnnByLabel.getState();
680 sortAnnBySequence.setSelected(false);
681 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
682 : SequenceAnnotationOrder.NONE);
683 sortAnnotations_actionPerformed();
686 colourTextMenuItem = new JCheckBoxMenuItem(
688 .getString("label.colour_text"));
689 colourTextMenuItem.addActionListener(new ActionListener()
692 public void actionPerformed(ActionEvent e)
694 colourTextMenuItem_actionPerformed(e);
698 JMenuItem htmlMenuItem = new JMenuItem(
699 MessageManager.getString("label.html"));
700 htmlMenuItem.addActionListener(new ActionListener()
703 public void actionPerformed(ActionEvent e)
705 htmlMenuItem_actionPerformed(e);
709 JMenuItem createBioJS = new JMenuItem(
710 MessageManager.getString("label.biojs_html_export"));
711 createBioJS.addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 bioJSMenuItem_actionPerformed(e);
720 JMenuItem overviewMenuItem = new JMenuItem(
721 MessageManager.getString("label.overview_window"));
722 overviewMenuItem.addActionListener(new ActionListener()
725 public void actionPerformed(ActionEvent e)
727 overviewMenuItem_actionPerformed(e);
731 undoMenuItem.setEnabled(false);
732 undoMenuItem.setText(MessageManager.getString("action.undo"));
733 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
734 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
735 al = new ActionListener()
738 public void actionPerformed(ActionEvent e)
740 undoMenuItem_actionPerformed(e);
743 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
745 redoMenuItem.setEnabled(false);
746 redoMenuItem.setText(MessageManager.getString("action.redo"));
747 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
748 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
749 al = new ActionListener()
752 public void actionPerformed(ActionEvent e)
754 redoMenuItem_actionPerformed(e);
757 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
759 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
760 wrapMenuItem.addActionListener(new ActionListener()
763 public void actionPerformed(ActionEvent e)
765 wrapMenuItem_actionPerformed(e);
769 JMenuItem printMenuItem = new JMenuItem(
770 MessageManager.getString("action.print"));
771 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
772 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
773 al = new ActionListener()
776 public void actionPerformed(ActionEvent e)
778 printMenuItem_actionPerformed(e);
781 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
784 .setText(MessageManager.getString("action.show_gaps"));
785 renderGapsMenuItem.setState(true);
786 renderGapsMenuItem.addActionListener(new ActionListener()
789 public void actionPerformed(ActionEvent e)
791 renderGapsMenuItem_actionPerformed(e);
795 JMenuItem findMenuItem = new JMenuItem(
796 MessageManager.getString("action.find"));
797 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
798 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
799 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
800 MessageManager.getString("label.find_tip")));
801 al = new ActionListener()
804 public void actionPerformed(ActionEvent e)
806 findMenuItem_actionPerformed(e);
809 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
811 showSeqFeatures.setText(MessageManager
812 .getString("label.show_sequence_features"));
813 showSeqFeatures.addActionListener(new ActionListener()
816 public void actionPerformed(ActionEvent actionEvent)
818 showSeqFeatures_actionPerformed(actionEvent);
822 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
823 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
824 * void actionPerformed(ActionEvent actionEvent) {
825 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
827 showDbRefsMenuitem.setText(MessageManager
828 .getString("label.show_database_refs"));
829 showDbRefsMenuitem.addActionListener(new ActionListener()
833 public void actionPerformed(ActionEvent e)
835 showDbRefs_actionPerformed(e);
839 showNpFeatsMenuitem.setText(MessageManager
840 .getString("label.show_non_positional_features"));
841 showNpFeatsMenuitem.addActionListener(new ActionListener()
845 public void actionPerformed(ActionEvent e)
847 showNpFeats_actionPerformed(e);
851 showGroupConservation.setText(MessageManager
852 .getString("label.group_conservation"));
853 showGroupConservation.addActionListener(new ActionListener()
857 public void actionPerformed(ActionEvent e)
859 showGroupConservation_actionPerformed(e);
864 showGroupConsensus.setText(MessageManager
865 .getString("label.group_consensus"));
866 showGroupConsensus.addActionListener(new ActionListener()
870 public void actionPerformed(ActionEvent e)
872 showGroupConsensus_actionPerformed(e);
876 showConsensusHistogram.setText(MessageManager
877 .getString("label.show_consensus_histogram"));
878 showConsensusHistogram.addActionListener(new ActionListener()
882 public void actionPerformed(ActionEvent e)
884 showConsensusHistogram_actionPerformed(e);
888 showSequenceLogo.setText(MessageManager
889 .getString("label.show_consensus_logo"));
890 showSequenceLogo.addActionListener(new ActionListener()
894 public void actionPerformed(ActionEvent e)
896 showSequenceLogo_actionPerformed(e);
900 normaliseSequenceLogo.setText(MessageManager
901 .getString("label.norm_consensus_logo"));
902 normaliseSequenceLogo.addActionListener(new ActionListener()
906 public void actionPerformed(ActionEvent e)
908 normaliseSequenceLogo_actionPerformed(e);
912 applyAutoAnnotationSettings.setText(MessageManager
913 .getString("label.apply_all_groups"));
914 applyAutoAnnotationSettings.setState(false);
915 applyAutoAnnotationSettings.setVisible(true);
916 applyAutoAnnotationSettings.addActionListener(new ActionListener()
919 public void actionPerformed(ActionEvent e)
921 applyAutoAnnotationSettings_actionPerformed(e);
925 ButtonGroup buttonGroup = new ButtonGroup();
926 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
927 MessageManager.getString("label.show_first"));
928 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
929 MessageManager.getString("label.show_last"));
930 buttonGroup.add(showAutoFirst);
931 buttonGroup.add(showAutoLast);
932 final boolean autoFirst = Cache.getDefault(
933 Preferences.SHOW_AUTOCALC_ABOVE, false);
934 showAutoFirst.setSelected(autoFirst);
935 setShowAutoCalculatedAbove(autoFirst);
936 showAutoFirst.addActionListener(new ActionListener()
939 public void actionPerformed(ActionEvent e)
941 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
942 sortAnnotations_actionPerformed();
945 showAutoLast.setSelected(!showAutoFirst.isSelected());
946 showAutoLast.addActionListener(new ActionListener()
949 public void actionPerformed(ActionEvent e)
951 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
952 sortAnnotations_actionPerformed();
956 JMenuItem deleteGroups = new JMenuItem(
957 MessageManager.getString("action.undefine_groups"));
958 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
959 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
960 al = new ActionListener()
963 public void actionPerformed(ActionEvent e)
965 deleteGroups_actionPerformed(e);
968 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
970 JMenuItem annotationColumn = new JMenuItem(
971 MessageManager.getString("action.select_by_annotation"));
972 annotationColumn.addActionListener(new ActionListener()
975 public void actionPerformed(ActionEvent e)
977 annotationColumn_actionPerformed(e);
981 createGroup = new JMenuItem(
982 MessageManager.getString("action.create_group"));
983 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
984 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
985 al = new ActionListener()
988 public void actionPerformed(ActionEvent e)
990 createGroup_actionPerformed(e);
993 addMenuActionAndAccelerator(keyStroke, createGroup, al);
995 unGroup = new JMenuItem(
996 MessageManager.getString("action.remove_group"));
997 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
998 .getDefaultToolkit().getMenuShortcutKeyMask()
999 | KeyEvent.SHIFT_MASK, false);
1000 al = new ActionListener()
1003 public void actionPerformed(ActionEvent e)
1005 unGroup_actionPerformed(e);
1008 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1010 copy.setText(MessageManager.getString("action.copy"));
1011 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1012 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1014 al = new ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 copy_actionPerformed(e);
1022 addMenuActionAndAccelerator(keyStroke, copy, al);
1024 cut.setText(MessageManager.getString("action.cut"));
1025 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1026 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1027 al = new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 cut_actionPerformed(e);
1035 addMenuActionAndAccelerator(keyStroke, cut, al);
1037 JMenuItem delete = new JMenuItem(
1038 MessageManager.getString("action.delete"));
1039 delete.addActionListener(new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 delete_actionPerformed(e);
1048 pasteMenu.setText(MessageManager.getString("action.paste"));
1049 JMenuItem pasteNew = new JMenuItem(
1050 MessageManager.getString("label.to_new_alignment"));
1051 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1052 .getDefaultToolkit().getMenuShortcutKeyMask()
1053 | KeyEvent.SHIFT_MASK, false);
1054 al = new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 pasteNew_actionPerformed(e);
1062 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1064 JMenuItem pasteThis = new JMenuItem(
1065 MessageManager.getString("label.to_this_alignment"));
1066 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1067 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1068 al = new ActionListener()
1071 public void actionPerformed(ActionEvent e)
1073 pasteThis_actionPerformed(e);
1076 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1078 JMenuItem createPNG = new JMenuItem("PNG");
1079 createPNG.addActionListener(new ActionListener()
1082 public void actionPerformed(ActionEvent e)
1087 createPNG.setActionCommand(MessageManager
1088 .getString("label.save_png_image"));
1090 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1091 font.addActionListener(new ActionListener()
1094 public void actionPerformed(ActionEvent e)
1096 font_actionPerformed(e);
1099 seqLimits.setText(MessageManager
1100 .getString("label.show_sequence_limits"));
1101 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1102 seqLimits.addActionListener(new ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 seqLimit_actionPerformed(e);
1110 JMenuItem epsFile = new JMenuItem("EPS");
1111 epsFile.addActionListener(new ActionListener()
1114 public void actionPerformed(ActionEvent e)
1120 JMenuItem createSVG = new JMenuItem("SVG");
1121 createSVG.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1130 JMenuItem loadTreeMenuItem = new JMenuItem(
1131 MessageManager.getString("label.load_associated_tree"));
1132 loadTreeMenuItem.setActionCommand(MessageManager
1133 .getString("label.load_tree_for_sequence_set"));
1134 loadTreeMenuItem.addActionListener(new ActionListener()
1137 public void actionPerformed(ActionEvent e)
1139 loadTreeMenuItem_actionPerformed(e);
1143 scaleAbove.setVisible(false);
1144 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1145 scaleAbove.addActionListener(new ActionListener()
1148 public void actionPerformed(ActionEvent e)
1150 scaleAbove_actionPerformed(e);
1153 scaleLeft.setVisible(false);
1154 scaleLeft.setSelected(true);
1155 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1156 scaleLeft.addActionListener(new ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 scaleLeft_actionPerformed(e);
1164 scaleRight.setVisible(false);
1165 scaleRight.setSelected(true);
1166 scaleRight.setText(MessageManager.getString("action.scale_right"));
1167 scaleRight.addActionListener(new ActionListener()
1170 public void actionPerformed(ActionEvent e)
1172 scaleRight_actionPerformed(e);
1175 centreColumnLabelsMenuItem.setVisible(true);
1176 centreColumnLabelsMenuItem.setState(false);
1177 centreColumnLabelsMenuItem.setText(MessageManager
1178 .getString("label.centre_column_labels"));
1179 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1182 public void actionPerformed(ActionEvent e)
1184 centreColumnLabels_actionPerformed(e);
1187 followHighlightMenuItem.setVisible(true);
1188 followHighlightMenuItem.setState(true);
1189 followHighlightMenuItem.setText(MessageManager
1190 .getString("label.automatic_scrolling"));
1191 followHighlightMenuItem.addActionListener(new ActionListener()
1195 public void actionPerformed(ActionEvent e)
1197 followHighlight_actionPerformed();
1203 .setText(MessageManager.getString("action.by_tree_order"));
1204 sort.setText(MessageManager.getString("action.sort"));
1205 sort.addMenuListener(new MenuListener()
1208 public void menuSelected(MenuEvent e)
1214 public void menuDeselected(MenuEvent e)
1219 public void menuCanceled(MenuEvent e)
1223 sortByAnnotScore.setText(MessageManager
1224 .getString("label.sort_by_score"));
1225 sort.add(sortByAnnotScore);
1226 sort.addMenuListener(new javax.swing.event.MenuListener()
1230 public void menuCanceled(MenuEvent e)
1235 public void menuDeselected(MenuEvent e)
1240 public void menuSelected(MenuEvent e)
1242 buildSortByAnnotationScoresMenu();
1245 sortByAnnotScore.setVisible(false);
1248 .setText(MessageManager.getString("action.calculate_tree"));
1250 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1251 padGapsMenuitem.setState(jalview.bin.Cache
1252 .getDefault("PAD_GAPS", false));
1253 padGapsMenuitem.addActionListener(new ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 padGapsMenuitem_actionPerformed(e);
1261 JMenuItem vamsasStore = new JMenuItem(
1262 MessageManager.getString("label.vamsas_store"));
1263 vamsasStore.setVisible(false);
1264 vamsasStore.addActionListener(new ActionListener()
1267 public void actionPerformed(ActionEvent e)
1269 vamsasStore_actionPerformed(e);
1272 showTranslation.setText(MessageManager
1273 .getString("label.translate_cDNA"));
1274 showTranslation.addActionListener(new ActionListener()
1277 public void actionPerformed(ActionEvent e)
1279 showTranslation_actionPerformed(e);
1282 showReverse.setText(MessageManager.getString("label.reverse"));
1283 showReverse.addActionListener(new ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 showReverse_actionPerformed(false);
1291 showReverseComplement.setText(MessageManager
1292 .getString("label.reverse_complement"));
1293 showReverseComplement.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 showReverse_actionPerformed(true);
1302 JMenuItem extractScores = new JMenuItem(
1303 MessageManager.getString("label.extract_scores"));
1304 extractScores.addActionListener(new ActionListener()
1307 public void actionPerformed(ActionEvent e)
1309 extractScores_actionPerformed(e);
1312 extractScores.setVisible(true);
1313 // JBPNote: TODO: make gui for regex based score extraction
1315 // for show products actions see AlignFrame.canShowProducts
1316 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1318 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1319 runGroovy.setToolTipText(MessageManager
1320 .getString("label.run_groovy_tip"));
1321 runGroovy.addActionListener(new ActionListener()
1324 public void actionPerformed(ActionEvent e)
1326 runGroovy_actionPerformed();
1330 JMenuItem openFeatureSettings = new JMenuItem(
1331 MessageManager.getString("action.feature_settings"));
1332 openFeatureSettings.addActionListener(new ActionListener()
1335 public void actionPerformed(ActionEvent e)
1337 featureSettings_actionPerformed(e);
1340 JMenuItem fetchSequence = new JMenuItem(
1341 MessageManager.getString("label.fetch_sequences"));
1342 fetchSequence.addActionListener(new ActionListener()
1345 public void actionPerformed(ActionEvent e)
1347 fetchSequence_actionPerformed(e);
1351 JMenuItem associatedData = new JMenuItem(
1352 MessageManager.getString("label.load_features_annotations"));
1353 associatedData.addActionListener(new ActionListener()
1356 public void actionPerformed(ActionEvent e)
1358 associatedData_actionPerformed(e);
1361 autoCalculate.setText(MessageManager
1362 .getString("label.autocalculate_consensus"));
1363 autoCalculate.setState(jalview.bin.Cache.getDefault(
1364 "AUTO_CALC_CONSENSUS", true));
1365 autoCalculate.addActionListener(new ActionListener()
1368 public void actionPerformed(ActionEvent e)
1370 autoCalculate_actionPerformed(e);
1373 sortByTree.setText(MessageManager
1374 .getString("label.sort_alignment_new_tree"));
1376 .setToolTipText("<html>"
1378 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1380 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1381 sortByTree.addActionListener(new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 sortByTreeOption_actionPerformed(e);
1390 listenToViewSelections.setText(MessageManager
1391 .getString("label.listen_for_selections"));
1392 listenToViewSelections
1393 .setToolTipText("<html>"
1395 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1396 listenToViewSelections.setState(false);
1397 listenToViewSelections.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 listenToViewSelections_actionPerformed(e);
1406 JMenu addSequenceMenu = new JMenu(
1407 MessageManager.getString("label.add_sequences"));
1408 JMenuItem addFromFile = new JMenuItem(
1409 MessageManager.getString("label.from_file"));
1410 addFromFile.addActionListener(new ActionListener()
1413 public void actionPerformed(ActionEvent e)
1415 addFromFile_actionPerformed(e);
1418 JMenuItem addFromText = new JMenuItem(
1419 MessageManager.getString("label.from_textbox"));
1420 addFromText.addActionListener(new ActionListener()
1423 public void actionPerformed(ActionEvent e)
1425 addFromText_actionPerformed(e);
1428 JMenuItem addFromURL = new JMenuItem(
1429 MessageManager.getString("label.from_url"));
1430 addFromURL.addActionListener(new ActionListener()
1433 public void actionPerformed(ActionEvent e)
1435 addFromURL_actionPerformed(e);
1438 JMenuItem exportFeatures = new JMenuItem(
1439 MessageManager.getString("label.export_features"));
1440 exportFeatures.addActionListener(new ActionListener()
1443 public void actionPerformed(ActionEvent e)
1445 exportFeatures_actionPerformed(e);
1448 JMenuItem exportAnnotations = new JMenuItem(
1449 MessageManager.getString("label.export_annotations"));
1450 exportAnnotations.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 exportAnnotations_actionPerformed(e);
1458 statusPanel.setLayout(new GridLayout());
1459 JMenuItem showAllSeqs = new JMenuItem(
1460 MessageManager.getString("label.all_sequences"));
1461 showAllSeqs.setToolTipText(MessageManager
1462 .getString("label.toggle_sequence_visibility"));
1463 showAllSeqs.addActionListener(new ActionListener()
1466 public void actionPerformed(ActionEvent e)
1468 showAllSeqs_actionPerformed(e);
1471 JMenuItem showAllColumns = new JMenuItem(
1472 MessageManager.getString("label.all_columns"));
1473 showAllColumns.setToolTipText(MessageManager
1474 .getString("label.toggle_columns_visibility"));
1475 showAllColumns.addActionListener(new ActionListener()
1478 public void actionPerformed(ActionEvent e)
1480 showAllColumns_actionPerformed(e);
1483 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1484 JMenuItem hideSelSequences = new JMenuItem(
1485 MessageManager.getString("label.selected_sequences"));
1486 hideSelSequences.setToolTipText(MessageManager
1487 .getString("label.toggle_sequence_visibility"));
1488 hideSelSequences.addActionListener(new ActionListener()
1491 public void actionPerformed(ActionEvent e)
1493 hideSelSequences_actionPerformed(e);
1496 JMenuItem hideSelColumns = new JMenuItem(
1497 MessageManager.getString("label.selected_columns"));
1498 hideSelColumns.setToolTipText(MessageManager
1499 .getString("label.toggle_columns_visibility"));
1500 hideSelColumns.addActionListener(new ActionListener()
1503 public void actionPerformed(ActionEvent e)
1505 hideSelColumns_actionPerformed(e);
1508 JMenuItem hideAllSelection = new JMenuItem(
1509 MessageManager.getString("label.selected_region"));
1510 hideAllSelection.addActionListener(new ActionListener()
1513 public void actionPerformed(ActionEvent e)
1515 hideAllSelection_actionPerformed(e);
1518 // TODO: should be hidden if no selection exists.
1519 JMenuItem hideAllButSelection = new JMenuItem(
1520 MessageManager.getString("label.all_but_selected_region"));
1521 hideAllButSelection.addActionListener(new ActionListener()
1524 public void actionPerformed(ActionEvent e)
1526 hideAllButSelection_actionPerformed(e);
1529 JMenuItem showAllhidden = new JMenuItem(
1530 MessageManager.getString("label.all_sequences_columns"));
1531 showAllhidden.setToolTipText(MessageManager
1532 .getString("label.toggles_visibility_hidden_selected_regions"));
1533 showAllhidden.addActionListener(new ActionListener()
1536 public void actionPerformed(ActionEvent e)
1538 showAllhidden_actionPerformed(e);
1541 hiddenMarkers.setText(MessageManager
1542 .getString("action.show_hidden_markers"));
1543 hiddenMarkers.addActionListener(new ActionListener()
1546 public void actionPerformed(ActionEvent e)
1548 hiddenMarkers_actionPerformed(e);
1552 JMenuItem invertColSel = new JMenuItem(
1553 MessageManager.getString("action.invert_column_selection"));
1554 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1555 .getDefaultToolkit().getMenuShortcutKeyMask()
1556 | KeyEvent.ALT_MASK, false);
1557 al = new ActionListener()
1560 public void actionPerformed(ActionEvent e)
1562 invertColSel_actionPerformed(e);
1565 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1567 showComplementMenuItem.setVisible(false);
1568 showComplementMenuItem.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 showComplement_actionPerformed(showComplementMenuItem.getState());
1577 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1580 public void stateChanged(ChangeEvent evt)
1582 JTabbedPane pane = (JTabbedPane) evt.getSource();
1583 int sel = pane.getSelectedIndex();
1584 tabSelectionChanged(sel);
1587 tabbedPane.addMouseListener(new MouseAdapter()
1590 public void mousePressed(MouseEvent e)
1592 if (e.isPopupTrigger()) // Mac
1594 tabbedPane_mousePressed(e);
1599 public void mouseReleased(MouseEvent e)
1601 if (e.isPopupTrigger()) // Windows
1603 tabbedPane_mousePressed(e);
1607 tabbedPane.addFocusListener(new FocusAdapter()
1610 public void focusGained(FocusEvent e)
1612 tabbedPane_focusGained(e);
1616 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1617 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1618 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1619 al = new ActionListener()
1622 public void actionPerformed(ActionEvent e)
1624 save_actionPerformed(e);
1627 addMenuActionAndAccelerator(keyStroke, save, al);
1629 reload.setEnabled(false);
1630 reload.setText(MessageManager.getString("action.reload"));
1631 reload.addActionListener(new ActionListener()
1634 public void actionPerformed(ActionEvent e)
1636 reload_actionPerformed(e);
1640 JMenuItem newView = new JMenuItem(
1641 MessageManager.getString("action.new_view"));
1642 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1643 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1644 al = new ActionListener()
1647 public void actionPerformed(ActionEvent e)
1649 newView_actionPerformed(e);
1652 addMenuActionAndAccelerator(keyStroke, newView, al);
1654 tabbedPane.setToolTipText("<html><i>"
1655 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1658 formatMenu.setText(MessageManager.getString("action.format"));
1659 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1660 selectMenu.addMenuListener(new MenuListener()
1663 public void menuSelected(MenuEvent e)
1665 configureSelectMenu();
1669 public void menuDeselected(MenuEvent e)
1674 public void menuCanceled(MenuEvent e)
1678 idRightAlign.setText(MessageManager
1679 .getString("label.right_align_sequence_id"));
1680 idRightAlign.addActionListener(new ActionListener()
1683 public void actionPerformed(ActionEvent e)
1685 idRightAlign_actionPerformed(e);
1689 gatherViews.setEnabled(false);
1690 gatherViews.setText(MessageManager.getString("action.gather_views"));
1691 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1692 al = new ActionListener()
1695 public void actionPerformed(ActionEvent e)
1697 gatherViews_actionPerformed(e);
1700 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1702 expandViews.setEnabled(false);
1703 expandViews.setText(MessageManager.getString("action.expand_views"));
1704 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1705 al = new ActionListener()
1708 public void actionPerformed(ActionEvent e)
1710 expandViews_actionPerformed(e);
1713 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1715 JMenuItem pageSetup = new JMenuItem(
1716 MessageManager.getString("action.page_setup"));
1717 pageSetup.addActionListener(new ActionListener()
1720 public void actionPerformed(ActionEvent e)
1722 pageSetup_actionPerformed(e);
1725 JMenuItem alignmentProperties = new JMenuItem(
1726 MessageManager.getString("label.alignment_props"));
1727 alignmentProperties.addActionListener(new ActionListener()
1730 public void actionPerformed(ActionEvent actionEvent)
1732 alignmentProperties();
1735 JMenuItem selectHighlighted = new JMenuItem(
1736 MessageManager.getString("action.select_highlighted_columns"));
1737 selectHighlighted.setToolTipText(MessageManager
1738 .getString("tooltip.select_highlighted_columns"));
1739 al = new ActionListener()
1742 public void actionPerformed(ActionEvent actionEvent)
1744 selectHighlightedColumns_actionPerformed(actionEvent);
1747 selectHighlighted.addActionListener(al);
1748 JMenu tooltipSettingsMenu = new JMenu(
1749 MessageManager.getString("label.sequence_id_tooltip"));
1750 JMenu autoAnnMenu = new JMenu(
1751 MessageManager.getString("label.autocalculated_annotation"));
1753 JMenu exportImageMenu = new JMenu(
1754 MessageManager.getString("label.export_image"));
1755 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1756 alignFrameMenuBar.add(fileMenu);
1757 alignFrameMenuBar.add(editMenu);
1758 alignFrameMenuBar.add(selectMenu);
1759 alignFrameMenuBar.add(viewMenu);
1760 alignFrameMenuBar.add(annotationsMenu);
1761 alignFrameMenuBar.add(formatMenu);
1762 alignFrameMenuBar.add(colourMenu);
1763 alignFrameMenuBar.add(calculateMenu);
1764 alignFrameMenuBar.add(webService);
1766 fileMenu.add(fetchSequence);
1767 fileMenu.add(addSequenceMenu);
1768 fileMenu.add(reload);
1769 fileMenu.addSeparator();
1770 fileMenu.add(vamsasStore);
1772 fileMenu.add(saveAs);
1773 fileMenu.add(outputTextboxMenu);
1774 fileMenu.add(pageSetup);
1775 fileMenu.add(printMenuItem);
1776 fileMenu.addSeparator();
1777 fileMenu.add(exportImageMenu);
1778 fileMenu.add(exportFeatures);
1779 fileMenu.add(exportAnnotations);
1780 fileMenu.add(loadTreeMenuItem);
1781 fileMenu.add(associatedData);
1782 fileMenu.addSeparator();
1783 fileMenu.add(closeMenuItem);
1785 pasteMenu.add(pasteNew);
1786 pasteMenu.add(pasteThis);
1787 editMenu.add(undoMenuItem);
1788 editMenu.add(redoMenuItem);
1791 editMenu.add(pasteMenu);
1792 editMenu.add(delete);
1793 editMenu.addSeparator();
1794 editMenu.add(remove2LeftMenuItem);
1795 editMenu.add(remove2RightMenuItem);
1796 editMenu.add(removeGappedColumnMenuItem);
1797 editMenu.add(removeAllGapsMenuItem);
1798 editMenu.add(removeRedundancyMenuItem);
1799 editMenu.addSeparator();
1800 // dont add these yet in the CVS build - they cannot be undone!
1801 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1802 // editMenu.add(justifyLeftMenuItem);
1803 // editMenu.add(justifyRightMenuItem);
1804 // editMenu.addSeparator();
1805 editMenu.add(padGapsMenuitem);
1807 showMenu.add(showAllColumns);
1808 showMenu.add(showAllSeqs);
1809 showMenu.add(showAllhidden);
1810 hideMenu.add(hideSelColumns);
1811 hideMenu.add(hideSelSequences);
1812 hideMenu.add(hideAllSelection);
1813 hideMenu.add(hideAllButSelection);
1814 viewMenu.add(newView);
1815 viewMenu.add(expandViews);
1816 viewMenu.add(gatherViews);
1817 viewMenu.addSeparator();
1818 viewMenu.add(showMenu);
1819 viewMenu.add(hideMenu);
1820 viewMenu.add(showComplementMenuItem);
1821 viewMenu.addSeparator();
1822 viewMenu.add(followHighlightMenuItem);
1823 viewMenu.addSeparator();
1824 viewMenu.add(showSeqFeatures);
1825 // viewMenu.add(showSeqFeaturesHeight);
1826 viewMenu.add(openFeatureSettings);
1827 tooltipSettingsMenu.add(showDbRefsMenuitem);
1828 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1829 viewMenu.add(tooltipSettingsMenu);
1830 viewMenu.addSeparator();
1831 viewMenu.add(alignmentProperties);
1832 viewMenu.addSeparator();
1833 viewMenu.add(overviewMenuItem);
1835 annotationsMenu.add(annotationPanelMenuItem);
1836 annotationsMenu.addSeparator();
1837 annotationsMenu.add(showAllAlAnnotations);
1838 annotationsMenu.add(hideAllAlAnnotations);
1839 annotationsMenu.addSeparator();
1840 annotationsMenu.add(showAllSeqAnnotations);
1841 annotationsMenu.add(hideAllSeqAnnotations);
1842 annotationsMenu.add(sortAnnBySequence);
1843 annotationsMenu.add(sortAnnByLabel);
1844 annotationsMenu.addSeparator();
1845 autoAnnMenu.add(showAutoFirst);
1846 autoAnnMenu.add(showAutoLast);
1847 autoAnnMenu.addSeparator();
1848 autoAnnMenu.add(applyAutoAnnotationSettings);
1849 autoAnnMenu.add(showConsensusHistogram);
1850 autoAnnMenu.add(showSequenceLogo);
1851 autoAnnMenu.add(normaliseSequenceLogo);
1852 autoAnnMenu.addSeparator();
1853 autoAnnMenu.add(showGroupConservation);
1854 autoAnnMenu.add(showGroupConsensus);
1855 annotationsMenu.add(autoAnnMenu);
1858 sort.add(sortIDMenuItem);
1859 sort.add(sortLengthMenuItem);
1860 sort.add(sortGroupMenuItem);
1861 sort.add(sortPairwiseMenuItem);
1862 sort.add(sortByTreeMenu);
1863 calculateMenu.add(sort);
1864 calculateMenu.add(calculateTree);
1865 calculateMenu.addSeparator();
1866 calculateMenu.add(pairwiseAlignmentMenuItem);
1867 calculateMenu.add(PCAMenuItem);
1868 calculateMenu.addSeparator();
1869 calculateMenu.add(showTranslation);
1870 calculateMenu.add(showReverse);
1871 calculateMenu.add(showReverseComplement);
1872 calculateMenu.add(showProducts);
1873 calculateMenu.add(autoCalculate);
1874 calculateMenu.add(sortByTree);
1875 calculateMenu.addSeparator();
1876 calculateMenu.add(expandAlignment);
1877 calculateMenu.add(extractScores);
1878 calculateMenu.addSeparator();
1879 calculateMenu.add(runGroovy);
1881 webServiceNoServices = new JMenuItem(
1882 MessageManager.getString("label.no_services"));
1883 webService.add(webServiceNoServices);
1884 exportImageMenu.add(htmlMenuItem);
1885 exportImageMenu.add(epsFile);
1886 exportImageMenu.add(createPNG);
1887 exportImageMenu.add(createBioJS);
1888 exportImageMenu.add(createSVG);
1889 addSequenceMenu.add(addFromFile);
1890 addSequenceMenu.add(addFromText);
1891 addSequenceMenu.add(addFromURL);
1892 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1893 statusPanel.add(statusBar, null);
1894 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1896 formatMenu.add(font);
1897 formatMenu.addSeparator();
1898 formatMenu.add(wrapMenuItem);
1899 formatMenu.add(scaleAbove);
1900 formatMenu.add(scaleLeft);
1901 formatMenu.add(scaleRight);
1902 formatMenu.add(seqLimits);
1903 formatMenu.add(idRightAlign);
1904 formatMenu.add(hiddenMarkers);
1905 formatMenu.add(viewBoxesMenuItem);
1906 formatMenu.add(viewTextMenuItem);
1907 formatMenu.add(colourTextMenuItem);
1908 formatMenu.add(renderGapsMenuItem);
1909 formatMenu.add(centreColumnLabelsMenuItem);
1910 formatMenu.add(showNonconservedMenuItem);
1911 selectMenu.add(findMenuItem);
1912 selectMenu.addSeparator();
1913 selectMenu.add(selectAllSequenceMenuItem);
1914 selectMenu.add(deselectAllSequenceMenuItem);
1915 selectMenu.add(invertSequenceMenuItem);
1916 selectMenu.add(invertColSel);
1917 selectMenu.add(createGroup);
1918 selectMenu.add(unGroup);
1919 selectMenu.add(grpsFromSelection);
1920 selectMenu.add(deleteGroups);
1921 selectMenu.add(annotationColumn);
1922 selectMenu.add(selectHighlighted);
1923 // TODO - determine if the listenToViewSelections button is needed : see bug
1925 // selectMenu.addSeparator();
1926 // selectMenu.add(listenToViewSelections);
1929 protected void configureSelectMenu()
1931 // TODO Auto-generated method stub
1936 * Constructs the entries on the Colour menu (but does not add them to the
1939 protected void initColourMenu()
1941 applyToAllGroups = new JCheckBoxMenuItem(
1942 MessageManager.getString("label.apply_colour_to_all_groups"));
1943 applyToAllGroups.addActionListener(new ActionListener()
1946 public void actionPerformed(ActionEvent e)
1948 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1952 textColour = new JRadioButtonMenuItem(
1953 MessageManager.getString("action.set_text_colour"));
1954 textColour.addActionListener(new ActionListener()
1957 public void actionPerformed(ActionEvent e)
1959 textColour_actionPerformed();
1963 conservationMenuItem = new JCheckBoxMenuItem(
1964 MessageManager.getString("action.by_conservation"));
1965 conservationMenuItem.addActionListener(new ActionListener()
1968 public void actionPerformed(ActionEvent e)
1970 conservationMenuItem_actionPerformed(conservationMenuItem
1975 abovePIDThreshold = new JCheckBoxMenuItem(
1976 MessageManager.getString("label.above_identity_threshold"));
1977 abovePIDThreshold.addActionListener(new ActionListener()
1980 public void actionPerformed(ActionEvent e)
1982 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1985 modifyPID = new JMenuItem(
1986 MessageManager.getString("label.modify_identity_threshold"));
1987 modifyPID.addActionListener(new ActionListener()
1990 public void actionPerformed(ActionEvent e)
1992 modifyPID_actionPerformed();
1995 modifyConservation = new JMenuItem(
1997 .getString("label.modify_conservation_threshold"));
1998 modifyConservation.addActionListener(new ActionListener()
2001 public void actionPerformed(ActionEvent e)
2003 modifyConservation_actionPerformed();
2007 annotationColour = new JMenuItem(
2008 MessageManager.getString("action.by_annotation"));
2009 annotationColour.addActionListener(new ActionListener()
2012 public void actionPerformed(ActionEvent e)
2014 annotationColour_actionPerformed();
2019 protected void selectHighlightedColumns_actionPerformed(
2020 ActionEvent actionEvent)
2022 // TODO Auto-generated method stub
2027 * Generate the reverse sequence (or reverse complement if the flag is true)
2028 * and add it to the alignment
2032 protected void showReverse_actionPerformed(boolean complement)
2037 * Try to run script in a Groovy console, having first ensured that this
2038 * alignframe is set as currentAlignFrame in Desktop
2040 protected void runGroovy_actionPerformed()
2046 * Adds the given action listener and key accelerator to the given menu item.
2047 * Also saves in a lookup table to support lookup of action by key stroke.
2051 * @param actionListener
2053 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2054 JMenuItem menuItem, ActionListener actionListener)
2056 menuItem.setAccelerator(keyStroke);
2057 accelerators.put(keyStroke, menuItem);
2058 menuItem.addActionListener(actionListener);
2062 * Action on clicking sort annotations by type.
2066 protected void sortAnnotations_actionPerformed()
2071 * Action on clicking Show all annotations.
2073 * @param forSequences
2074 * update sequence-related annotations
2075 * @param forAlignment
2076 * update non-sequence-related annotations
2078 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2079 boolean forAlignment)
2081 setAnnotationsVisibility(true, forSequences, forAlignment);
2085 * Action on clicking Hide all annotations.
2087 * @param forSequences
2088 * update sequence-related annotations
2089 * @param forAlignment
2090 * update non-sequence-related annotations
2092 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2093 boolean forAlignment)
2095 setAnnotationsVisibility(false, forSequences, forAlignment);
2099 * Set the visibility of annotations to true or false. Can act on
2100 * sequence-related annotations, or alignment-related, or both.
2103 * @param forSequences
2104 * update sequence-related annotations
2105 * @param forAlignment
2106 * update non-sequence-related annotations
2108 protected void setAnnotationsVisibility(boolean visible,
2109 boolean forSequences, boolean forAlignment)
2114 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2116 // TODO Auto-generated method stub
2120 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2122 // TODO Auto-generated method stub
2126 protected void showAllhidden_actionPerformed(ActionEvent e)
2128 // TODO Auto-generated method stub
2132 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2134 // TODO Auto-generated method stub
2138 protected void hideAllSelection_actionPerformed(ActionEvent e)
2140 // TODO Auto-generated method stub
2144 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2146 // TODO Auto-generated method stub
2150 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2152 // TODO Auto-generated method stub
2156 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2158 // TODO Auto-generated method stub
2162 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2164 // TODO Auto-generated method stub
2168 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2170 // TODO Auto-generated method stub
2174 protected void showGroupConservation_actionPerformed(ActionEvent e)
2176 // TODO Auto-generated method stub
2180 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2182 // TODO Auto-generated method stub
2186 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2188 // TODO Auto-generated method stub
2192 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2194 // TODO Auto-generated method stub
2198 protected void followHighlight_actionPerformed()
2200 // TODO Auto-generated method stub
2204 protected void showNpFeats_actionPerformed(ActionEvent e)
2206 // TODO Auto-generated method stub
2210 protected void showDbRefs_actionPerformed(ActionEvent e)
2212 // TODO Auto-generated method stub
2216 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2220 protected void buildSortByAnnotationScoresMenu()
2224 protected void extractScores_actionPerformed(ActionEvent e)
2228 protected void outputText_actionPerformed(ActionEvent e)
2232 public void addFromFile_actionPerformed(ActionEvent e)
2237 public void addFromText_actionPerformed(ActionEvent e)
2242 public void addFromURL_actionPerformed(ActionEvent e)
2247 public void exportFeatures_actionPerformed(ActionEvent e)
2252 public void exportAnnotations_actionPerformed(ActionEvent e)
2257 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2261 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2266 protected void closeMenuItem_actionPerformed(boolean b)
2270 protected void redoMenuItem_actionPerformed(ActionEvent e)
2274 protected void undoMenuItem_actionPerformed(ActionEvent e)
2278 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2282 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2286 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2290 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2294 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2298 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2302 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2306 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2310 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2314 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2318 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2322 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2326 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2330 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2334 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2338 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2342 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2346 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2350 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2354 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2358 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2362 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2366 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2370 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2374 protected void conservationMenuItem_actionPerformed(boolean selected)
2378 protected void printMenuItem_actionPerformed(ActionEvent e)
2382 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2386 protected void findMenuItem_actionPerformed(ActionEvent e)
2390 protected void abovePIDThreshold_actionPerformed(boolean selected)
2394 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2398 protected void deleteGroups_actionPerformed(ActionEvent e)
2402 protected void createGroup_actionPerformed(ActionEvent e)
2406 protected void unGroup_actionPerformed(ActionEvent e)
2410 protected void copy_actionPerformed(ActionEvent e)
2414 protected void cut_actionPerformed(ActionEvent e)
2418 protected void delete_actionPerformed(ActionEvent e)
2422 protected void pasteNew_actionPerformed(ActionEvent e)
2426 protected void pasteThis_actionPerformed(ActionEvent e)
2430 protected void applyToAllGroups_actionPerformed(boolean selected)
2434 public void createPNG(java.io.File f)
2438 protected void font_actionPerformed(ActionEvent e)
2442 protected void seqLimit_actionPerformed(ActionEvent e)
2446 public void seqDBRef_actionPerformed(ActionEvent e)
2451 public void createEPS(java.io.File f)
2455 public void createSVG(java.io.File f)
2460 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2466 * Template method to handle the 'load T-Coffee scores' menu event.
2468 * Subclasses override this method to provide a custom action.
2473 protected void loadScores_actionPerformed(ActionEvent event)
2478 protected void jpred_actionPerformed(ActionEvent e)
2482 protected void scaleAbove_actionPerformed(ActionEvent e)
2486 protected void scaleLeft_actionPerformed(ActionEvent e)
2490 protected void scaleRight_actionPerformed(ActionEvent e)
2494 protected void modifyPID_actionPerformed()
2498 protected void modifyConservation_actionPerformed()
2502 protected void saveAs_actionPerformed(ActionEvent e)
2506 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2510 public void vamsasStore_actionPerformed(ActionEvent e)
2515 public void vamsasLoad_actionPerformed(ActionEvent e)
2520 public void showTranslation_actionPerformed(ActionEvent e)
2525 public void featureSettings_actionPerformed(ActionEvent e)
2530 public void fetchSequence_actionPerformed(ActionEvent e)
2535 public void smoothFont_actionPerformed(ActionEvent e)
2540 public void annotationColour_actionPerformed()
2544 public void annotationColumn_actionPerformed(ActionEvent e)
2548 public void associatedData_actionPerformed(ActionEvent e)
2553 public void autoCalculate_actionPerformed(ActionEvent e)
2558 public void sortByTreeOption_actionPerformed(ActionEvent e)
2563 public void showAllSeqs_actionPerformed(ActionEvent e)
2568 public void showAllColumns_actionPerformed(ActionEvent e)
2573 public void hideSelSequences_actionPerformed(ActionEvent e)
2578 public void hideSelColumns_actionPerformed(ActionEvent e)
2583 public void hiddenMarkers_actionPerformed(ActionEvent e)
2588 public void findPdbId_actionPerformed(ActionEvent e)
2593 public void enterPdbId_actionPerformed(ActionEvent e)
2598 public void pdbFile_actionPerformed(ActionEvent e)
2603 public void invertColSel_actionPerformed(ActionEvent e)
2608 public void tabSelectionChanged(int sel)
2613 public void tabbedPane_mousePressed(MouseEvent e)
2618 public void tabbedPane_focusGained(FocusEvent e)
2623 public void save_actionPerformed(ActionEvent e)
2628 public void reload_actionPerformed(ActionEvent e)
2633 public void newView_actionPerformed(ActionEvent e)
2638 public void textColour_actionPerformed()
2643 public void idRightAlign_actionPerformed(ActionEvent e)
2648 public void expandViews_actionPerformed(ActionEvent e)
2653 public void gatherViews_actionPerformed(ActionEvent e)
2658 public void buildTreeMenu()
2663 public void pageSetup_actionPerformed(ActionEvent e)
2668 public void alignmentProperties()
2673 protected void expand_newalign(ActionEvent e)
2675 // TODO Auto-generated method stub
2679 protected boolean isShowAutoCalculatedAbove()
2681 return showAutoCalculatedAbove;
2684 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2686 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2689 protected SequenceAnnotationOrder getAnnotationSortOrder()
2691 return annotationSortOrder;
2694 protected void setAnnotationSortOrder(
2695 SequenceAnnotationOrder annotationSortOrder)
2697 this.annotationSortOrder = annotationSortOrder;
2700 public Map<KeyStroke, JMenuItem> getAccelerators()
2702 return this.accelerators;
2706 * Returns the selected index of the tabbed pane, or -1 if none selected
2707 * (including the case where the tabbed pane has not been made visible).
2711 public int getTabIndex()
2713 return tabbedPane.getSelectedIndex();
2716 public JPanel getStatusPanel()
2722 * Sets a reference to the containing split frame. Also makes the 'toggle
2723 * split view' menu item visible and checked.
2727 public void setSplitFrame(SplitContainerI sf)
2729 this.splitFrame = sf;
2732 this.showComplementMenuItem.setVisible(true);
2733 this.showComplementMenuItem.setState(true);
2737 public SplitContainerI getSplitViewContainer()
2739 return this.splitFrame;
2742 protected void showComplement_actionPerformed(boolean complement)