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 JMenu hmmerMenu = new JMenu();
72 protected JCheckBoxMenuItem autoAlignSeqs = new JCheckBoxMenuItem();
74 protected JMenuItem hmmAlign = new JMenuItem();
76 protected JMenuItem hmmSearch = new JMenuItem();
78 protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
80 protected JMenuItem webServiceNoServices;
82 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
84 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
86 protected JMenu sortByAnnotScore = new JMenu();
88 public JLabel statusBar = new JLabel();
90 protected JMenu outputTextboxMenu = new JMenu();
92 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
94 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
96 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
98 protected JMenuItem undoMenuItem = new JMenuItem();
100 protected JMenuItem redoMenuItem = new JMenuItem();
102 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
104 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
106 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
108 JMenuItem copy = new JMenuItem();
110 JMenuItem cut = new JMenuItem();
112 JMenu pasteMenu = new JMenu();
114 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
116 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
118 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
120 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
122 protected JCheckBoxMenuItem applyToAllGroups;
124 protected JMenu colourMenu = new JMenu();
126 protected JMenuItem textColour;
128 protected JCheckBoxMenuItem conservationMenuItem;
130 protected JMenuItem modifyConservation;
132 protected JCheckBoxMenuItem abovePIDThreshold;
134 protected JMenuItem modifyPID;
136 protected JMenuItem annotationColour;
138 protected JMenu sortByTreeMenu = new JMenu();
140 protected JMenu sort = new JMenu();
142 protected JMenuItem calculateTree = new JMenuItem();
144 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
146 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
148 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
150 protected JMenuItem showTranslation = new JMenuItem();
152 protected JMenuItem showReverse = new JMenuItem();
154 protected JMenuItem showReverseComplement = new JMenuItem();
156 protected JMenu showProducts = new JMenu();
158 protected JMenuItem runGroovy = new JMenuItem();
160 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
162 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
164 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
166 protected JPanel statusPanel = new JPanel();
168 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
170 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
172 protected JMenuItem showAllAlAnnotations = new JMenuItem();
174 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
176 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
178 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
180 protected JTabbedPane tabbedPane = new JTabbedPane();
182 protected JMenuItem reload = new JMenuItem();
184 protected JMenu formatMenu = new JMenu();
186 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
188 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
190 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
192 protected JMenuItem gatherViews = new JMenuItem();
194 protected JMenuItem expandViews = new JMenuItem();
196 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
198 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
200 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
202 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
204 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
206 protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
208 protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
210 protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
212 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
214 private SequenceAnnotationOrder annotationSortOrder;
216 private boolean showAutoCalculatedAbove = false;
218 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
220 private SplitContainerI splitFrame;
227 setJMenuBar(alignFrameMenuBar);
229 // dynamically fill save as menu with available formats
230 for (String ff : FileFormats.getInstance().getWritableFormats(true))
232 JMenuItem item = new JMenuItem(ff);
234 item.addActionListener(new ActionListener()
237 public void actionPerformed(ActionEvent e)
239 outputText_actionPerformed(e);
243 outputTextboxMenu.add(item);
245 } catch (Exception e)
247 System.err.println(e.toString());
250 if (!Platform.isAMac())
252 closeMenuItem.setMnemonic('C');
253 outputTextboxMenu.setMnemonic('T');
254 undoMenuItem.setMnemonic('Z');
255 redoMenuItem.setMnemonic('0');
256 copy.setMnemonic('C');
257 cut.setMnemonic('U');
258 pasteMenu.setMnemonic('P');
259 reload.setMnemonic('R');
263 private void jbInit() throws Exception
268 JMenuItem saveAs = new JMenuItem(
269 MessageManager.getString("action.save_as"));
270 ActionListener al = new ActionListener()
273 public void actionPerformed(ActionEvent e)
275 saveAs_actionPerformed(e);
279 // FIXME getDefaultToolkit throws an exception in Headless mode
280 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
281 .getDefaultToolkit().getMenuShortcutKeyMask()
282 | KeyEvent.SHIFT_MASK, false);
283 addMenuActionAndAccelerator(keyStroke, saveAs, al);
285 closeMenuItem.setText(MessageManager.getString("action.close"));
286 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
287 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
288 al = new ActionListener()
291 public void actionPerformed(ActionEvent e)
293 closeMenuItem_actionPerformed(false);
296 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
298 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
299 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
300 JMenu annotationsMenu = new JMenu(
301 MessageManager.getString("action.annotations"));
302 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
303 colourMenu.setText(MessageManager.getString("action.colour"));
304 JMenu calculateMenu = new JMenu(
305 MessageManager.getString("action.calculate"));
306 webService.setText(MessageManager.getString("action.web_service"));
307 hmmerMenu.setText(MessageManager.getString("action.hmmer"));
308 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
309 MessageManager.getString("action.select_all"));
310 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
311 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
312 al = new ActionListener()
315 public void actionPerformed(ActionEvent e)
317 selectAllSequenceMenuItem_actionPerformed(e);
320 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
322 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
323 MessageManager.getString("action.deselect_all"));
324 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
325 al = new ActionListener()
328 public void actionPerformed(ActionEvent e)
330 deselectAllSequenceMenuItem_actionPerformed(e);
333 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
335 JMenuItem invertSequenceMenuItem = new JMenuItem(
336 MessageManager.getString("action.invert_sequence_selection"));
337 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
338 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
339 al = new ActionListener()
342 public void actionPerformed(ActionEvent e)
344 invertSequenceMenuItem_actionPerformed(e);
347 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
349 JMenuItem grpsFromSelection = new JMenuItem(
350 MessageManager.getString("action.make_groups_selection"));
351 grpsFromSelection.addActionListener(new ActionListener()
354 public void actionPerformed(ActionEvent e)
356 makeGrpsFromSelection_actionPerformed(e);
359 JMenuItem expandAlignment = new JMenuItem(
360 MessageManager.getString("action.view_flanking_regions"));
361 expandAlignment.setToolTipText(MessageManager
362 .getString("label.view_flanking_regions"));
363 expandAlignment.addActionListener(new ActionListener()
366 public void actionPerformed(ActionEvent e)
371 JMenuItem remove2LeftMenuItem = new JMenuItem(
372 MessageManager.getString("action.remove_left"));
373 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
374 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
375 al = new ActionListener()
378 public void actionPerformed(ActionEvent e)
380 remove2LeftMenuItem_actionPerformed(e);
383 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
385 JMenuItem remove2RightMenuItem = new JMenuItem(
386 MessageManager.getString("action.remove_right"));
387 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
388 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
389 al = new ActionListener()
392 public void actionPerformed(ActionEvent e)
394 remove2RightMenuItem_actionPerformed(e);
397 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
399 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
400 MessageManager.getString("action.remove_empty_columns"));
401 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
402 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
403 al = new ActionListener()
406 public void actionPerformed(ActionEvent e)
408 removeGappedColumnMenuItem_actionPerformed(e);
411 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
413 JMenuItem removeAllGapsMenuItem = new JMenuItem(
414 MessageManager.getString("action.remove_all_gaps"));
415 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
416 .getDefaultToolkit().getMenuShortcutKeyMask()
417 | KeyEvent.SHIFT_MASK, false);
418 al = new ActionListener()
421 public void actionPerformed(ActionEvent e)
423 removeAllGapsMenuItem_actionPerformed(e);
426 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
428 JMenuItem justifyLeftMenuItem = new JMenuItem(
429 MessageManager.getString("action.left_justify_alignment"));
430 justifyLeftMenuItem.addActionListener(new ActionListener()
433 public void actionPerformed(ActionEvent e)
435 justifyLeftMenuItem_actionPerformed(e);
438 JMenuItem justifyRightMenuItem = new JMenuItem(
439 MessageManager.getString("action.right_justify_alignment"));
440 justifyRightMenuItem.addActionListener(new ActionListener()
443 public void actionPerformed(ActionEvent e)
445 justifyRightMenuItem_actionPerformed(e);
448 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
449 viewBoxesMenuItem.setState(true);
450 viewBoxesMenuItem.addActionListener(new ActionListener()
453 public void actionPerformed(ActionEvent e)
455 viewBoxesMenuItem_actionPerformed(e);
458 viewTextMenuItem.setText(MessageManager.getString("action.text"));
459 viewTextMenuItem.setState(true);
460 viewTextMenuItem.addActionListener(new ActionListener()
463 public void actionPerformed(ActionEvent e)
465 viewTextMenuItem_actionPerformed(e);
468 showNonconservedMenuItem.setText(MessageManager
469 .getString("label.show_non_conserved"));
470 showNonconservedMenuItem.setState(false);
471 showNonconservedMenuItem.addActionListener(new ActionListener()
474 public void actionPerformed(ActionEvent e)
476 showUnconservedMenuItem_actionPerformed(e);
479 JMenuItem sortPairwiseMenuItem = new JMenuItem(
480 MessageManager.getString("action.by_pairwise_id"));
481 sortPairwiseMenuItem.addActionListener(new ActionListener()
484 public void actionPerformed(ActionEvent e)
486 sortPairwiseMenuItem_actionPerformed(e);
489 JMenuItem sortIDMenuItem = new JMenuItem(
490 MessageManager.getString("action.by_id"));
491 sortIDMenuItem.addActionListener(new ActionListener()
494 public void actionPerformed(ActionEvent e)
496 sortIDMenuItem_actionPerformed(e);
499 JMenuItem sortLengthMenuItem = new JMenuItem(
500 MessageManager.getString("action.by_length"));
501 sortLengthMenuItem.addActionListener(new ActionListener()
504 public void actionPerformed(ActionEvent e)
506 sortLengthMenuItem_actionPerformed(e);
509 JMenuItem sortGroupMenuItem = new JMenuItem(
510 MessageManager.getString("action.by_group"));
511 sortGroupMenuItem.addActionListener(new ActionListener()
514 public void actionPerformed(ActionEvent e)
516 sortGroupMenuItem_actionPerformed(e);
520 JMenuItem removeRedundancyMenuItem = new JMenuItem(
521 MessageManager.getString("action.remove_redundancy"));
522 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
523 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
524 al = new ActionListener()
527 public void actionPerformed(ActionEvent e)
529 removeRedundancyMenuItem_actionPerformed(e);
532 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
534 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
535 MessageManager.getString("action.pairwise_alignment"));
536 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
539 public void actionPerformed(ActionEvent e)
541 pairwiseAlignmentMenuItem_actionPerformed(e);
545 this.getContentPane().setLayout(new BorderLayout());
546 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
547 statusBar.setBackground(Color.white);
548 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
549 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
550 statusBar.setText(MessageManager.getString("label.status_bar"));
551 outputTextboxMenu.setText(MessageManager
552 .getString("label.out_to_textbox"));
554 annotationPanelMenuItem.setActionCommand("");
555 annotationPanelMenuItem.setText(MessageManager
556 .getString("label.show_annotations"));
557 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
559 annotationPanelMenuItem.addActionListener(new ActionListener()
562 public void actionPerformed(ActionEvent e)
564 annotationPanelMenuItem_actionPerformed(e);
567 showAllAlAnnotations.setText(MessageManager
568 .getString("label.show_all_al_annotations"));
569 final boolean isAnnotationPanelShown = annotationPanelMenuItem
571 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
572 showAllAlAnnotations.addActionListener(new ActionListener()
575 public void actionPerformed(ActionEvent e)
577 showAllAnnotations_actionPerformed(false, true);
580 hideAllAlAnnotations.setText(MessageManager
581 .getString("label.hide_all_al_annotations"));
582 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
583 hideAllAlAnnotations.addActionListener(new ActionListener()
586 public void actionPerformed(ActionEvent e)
588 hideAllAnnotations_actionPerformed(false, true);
591 showAllSeqAnnotations.setText(MessageManager
592 .getString("label.show_all_seq_annotations"));
593 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
594 showAllSeqAnnotations.addActionListener(new ActionListener()
597 public void actionPerformed(ActionEvent e)
599 showAllAnnotations_actionPerformed(true, false);
602 hideAllSeqAnnotations.setText(MessageManager
603 .getString("label.hide_all_seq_annotations"));
604 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
605 hideAllSeqAnnotations.addActionListener(new ActionListener()
608 public void actionPerformed(ActionEvent e)
610 hideAllAnnotations_actionPerformed(true, false);
613 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
614 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
615 SequenceAnnotationOrder.NONE.name()));
616 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
617 MessageManager.getString("label.sort_annotations_by_sequence"));
618 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
619 MessageManager.getString("label.sort_annotations_by_label"));
622 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
623 sortAnnBySequence.addActionListener(new ActionListener()
626 public void actionPerformed(ActionEvent e)
628 boolean newState = sortAnnBySequence.getState();
629 sortAnnByLabel.setSelected(false);
630 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
631 : SequenceAnnotationOrder.NONE);
632 sortAnnotations_actionPerformed();
636 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
637 sortAnnByLabel.addActionListener(new ActionListener()
640 public void actionPerformed(ActionEvent e)
642 boolean newState = sortAnnByLabel.getState();
643 sortAnnBySequence.setSelected(false);
644 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
645 : SequenceAnnotationOrder.NONE);
646 sortAnnotations_actionPerformed();
649 colourTextMenuItem = new JCheckBoxMenuItem(
651 .getString("label.colour_text"));
652 colourTextMenuItem.addActionListener(new ActionListener()
655 public void actionPerformed(ActionEvent e)
657 colourTextMenuItem_actionPerformed(e);
661 JMenuItem htmlMenuItem = new JMenuItem(
662 MessageManager.getString("label.html"));
663 htmlMenuItem.addActionListener(new ActionListener()
666 public void actionPerformed(ActionEvent e)
668 htmlMenuItem_actionPerformed(e);
672 JMenuItem createBioJS = new JMenuItem(
673 MessageManager.getString("label.biojs_html_export"));
674 createBioJS.addActionListener(new java.awt.event.ActionListener()
677 public void actionPerformed(ActionEvent e)
679 bioJSMenuItem_actionPerformed(e);
683 JMenuItem overviewMenuItem = new JMenuItem(
684 MessageManager.getString("label.overview_window"));
685 overviewMenuItem.addActionListener(new ActionListener()
688 public void actionPerformed(ActionEvent e)
690 overviewMenuItem_actionPerformed(e);
694 undoMenuItem.setEnabled(false);
695 undoMenuItem.setText(MessageManager.getString("action.undo"));
696 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
697 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
698 al = new ActionListener()
701 public void actionPerformed(ActionEvent e)
703 undoMenuItem_actionPerformed(e);
706 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
708 redoMenuItem.setEnabled(false);
709 redoMenuItem.setText(MessageManager.getString("action.redo"));
710 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
711 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
712 al = new ActionListener()
715 public void actionPerformed(ActionEvent e)
717 redoMenuItem_actionPerformed(e);
720 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
722 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
723 wrapMenuItem.addActionListener(new ActionListener()
726 public void actionPerformed(ActionEvent e)
728 wrapMenuItem_actionPerformed(e);
732 JMenuItem printMenuItem = new JMenuItem(
733 MessageManager.getString("action.print"));
734 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
735 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
736 al = new ActionListener()
739 public void actionPerformed(ActionEvent e)
741 printMenuItem_actionPerformed(e);
744 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
747 .setText(MessageManager.getString("action.show_gaps"));
748 renderGapsMenuItem.setState(true);
749 renderGapsMenuItem.addActionListener(new ActionListener()
752 public void actionPerformed(ActionEvent e)
754 renderGapsMenuItem_actionPerformed(e);
758 JMenuItem findMenuItem = new JMenuItem(
759 MessageManager.getString("action.find"));
760 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
761 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
762 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
763 MessageManager.getString("label.find_tip")));
764 al = new ActionListener()
767 public void actionPerformed(ActionEvent e)
769 findMenuItem_actionPerformed(e);
772 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
774 showSeqFeatures.setText(MessageManager
775 .getString("label.show_sequence_features"));
776 showSeqFeatures.addActionListener(new ActionListener()
779 public void actionPerformed(ActionEvent actionEvent)
781 showSeqFeatures_actionPerformed(actionEvent);
785 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
786 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
787 * void actionPerformed(ActionEvent actionEvent) {
788 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
790 showDbRefsMenuitem.setText(MessageManager
791 .getString("label.show_database_refs"));
792 showDbRefsMenuitem.addActionListener(new ActionListener()
796 public void actionPerformed(ActionEvent e)
798 showDbRefs_actionPerformed(e);
802 showNpFeatsMenuitem.setText(MessageManager
803 .getString("label.show_non_positional_features"));
804 showNpFeatsMenuitem.addActionListener(new ActionListener()
808 public void actionPerformed(ActionEvent e)
810 showNpFeats_actionPerformed(e);
814 showGroupConservation.setText(MessageManager
815 .getString("label.group_conservation"));
816 showGroupConservation.addActionListener(new ActionListener()
820 public void actionPerformed(ActionEvent e)
822 showGroupConservation_actionPerformed(e);
827 showGroupConsensus.setText(MessageManager
828 .getString("label.group_consensus"));
829 showGroupConsensus.addActionListener(new ActionListener()
833 public void actionPerformed(ActionEvent e)
835 showGroupConsensus_actionPerformed(e);
839 showConsensusHistogram.setText(MessageManager
840 .getString("label.show_consensus_histogram"));
841 showConsensusHistogram.addActionListener(new ActionListener()
845 public void actionPerformed(ActionEvent e)
847 showConsensusHistogram_actionPerformed(e);
851 showSequenceLogo.setText(MessageManager
852 .getString("label.show_consensus_logo"));
853 showSequenceLogo.addActionListener(new ActionListener()
857 public void actionPerformed(ActionEvent e)
859 showSequenceLogo_actionPerformed(e);
863 normaliseSequenceLogo.setText(MessageManager
864 .getString("label.norm_consensus_logo"));
865 normaliseSequenceLogo.addActionListener(new ActionListener()
869 public void actionPerformed(ActionEvent e)
871 normaliseSequenceLogo_actionPerformed(e);
875 applyAutoAnnotationSettings.setText(MessageManager
876 .getString("label.apply_all_groups"));
877 applyAutoAnnotationSettings.setState(false);
878 applyAutoAnnotationSettings.setVisible(true);
879 applyAutoAnnotationSettings.addActionListener(new ActionListener()
882 public void actionPerformed(ActionEvent e)
884 applyAutoAnnotationSettings_actionPerformed(e);
888 ButtonGroup buttonGroup = new ButtonGroup();
889 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
890 MessageManager.getString("label.show_first"));
891 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
892 MessageManager.getString("label.show_last"));
893 buttonGroup.add(showAutoFirst);
894 buttonGroup.add(showAutoLast);
895 final boolean autoFirst = Cache.getDefault(
896 Preferences.SHOW_AUTOCALC_ABOVE, false);
897 showAutoFirst.setSelected(autoFirst);
898 setShowAutoCalculatedAbove(autoFirst);
899 showAutoFirst.addActionListener(new ActionListener()
902 public void actionPerformed(ActionEvent e)
904 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
905 sortAnnotations_actionPerformed();
908 showAutoLast.setSelected(!showAutoFirst.isSelected());
909 showAutoLast.addActionListener(new ActionListener()
912 public void actionPerformed(ActionEvent e)
914 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
915 sortAnnotations_actionPerformed();
919 JMenuItem deleteGroups = new JMenuItem(
920 MessageManager.getString("action.undefine_groups"));
921 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
922 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
923 al = new ActionListener()
926 public void actionPerformed(ActionEvent e)
928 deleteGroups_actionPerformed(e);
931 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
933 JMenuItem annotationColumn = new JMenuItem(
934 MessageManager.getString("action.select_by_annotation"));
935 annotationColumn.addActionListener(new ActionListener()
938 public void actionPerformed(ActionEvent e)
940 annotationColumn_actionPerformed(e);
944 JMenuItem createGroup = new JMenuItem(
945 MessageManager.getString("action.create_group"));
946 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
947 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
948 al = new ActionListener()
951 public void actionPerformed(ActionEvent e)
953 createGroup_actionPerformed(e);
956 addMenuActionAndAccelerator(keyStroke, createGroup, al);
958 JMenuItem unGroup = new JMenuItem(
959 MessageManager.getString("action.remove_group"));
960 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
961 .getDefaultToolkit().getMenuShortcutKeyMask()
962 | KeyEvent.SHIFT_MASK, false);
963 al = new ActionListener()
966 public void actionPerformed(ActionEvent e)
968 unGroup_actionPerformed(e);
971 addMenuActionAndAccelerator(keyStroke, unGroup, al);
973 copy.setText(MessageManager.getString("action.copy"));
974 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
975 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
977 al = new ActionListener()
980 public void actionPerformed(ActionEvent e)
982 copy_actionPerformed(e);
985 addMenuActionAndAccelerator(keyStroke, copy, al);
987 cut.setText(MessageManager.getString("action.cut"));
988 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
989 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
990 al = new ActionListener()
993 public void actionPerformed(ActionEvent e)
995 cut_actionPerformed(e);
998 addMenuActionAndAccelerator(keyStroke, cut, al);
1000 JMenuItem delete = new JMenuItem(
1001 MessageManager.getString("action.delete"));
1002 delete.addActionListener(new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 delete_actionPerformed(e);
1011 pasteMenu.setText(MessageManager.getString("action.paste"));
1012 JMenuItem pasteNew = new JMenuItem(
1013 MessageManager.getString("label.to_new_alignment"));
1014 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1015 .getDefaultToolkit().getMenuShortcutKeyMask()
1016 | KeyEvent.SHIFT_MASK, false);
1017 al = new ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 pasteNew_actionPerformed(e);
1025 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1027 JMenuItem pasteThis = new JMenuItem(
1028 MessageManager.getString("label.to_this_alignment"));
1029 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1030 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1031 al = new ActionListener()
1034 public void actionPerformed(ActionEvent e)
1036 pasteThis_actionPerformed(e);
1039 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1041 JMenuItem createPNG = new JMenuItem("PNG");
1042 createPNG.addActionListener(new ActionListener()
1045 public void actionPerformed(ActionEvent e)
1050 createPNG.setActionCommand(MessageManager
1051 .getString("label.save_png_image"));
1053 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1054 font.addActionListener(new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 font_actionPerformed(e);
1062 seqLimits.setText(MessageManager
1063 .getString("label.show_sequence_limits"));
1064 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1065 seqLimits.addActionListener(new ActionListener()
1068 public void actionPerformed(ActionEvent e)
1070 seqLimit_actionPerformed(e);
1073 JMenuItem epsFile = new JMenuItem("EPS");
1074 epsFile.addActionListener(new ActionListener()
1077 public void actionPerformed(ActionEvent e)
1083 JMenuItem createSVG = new JMenuItem("SVG");
1084 createSVG.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1093 JMenuItem loadTreeMenuItem = new JMenuItem(
1094 MessageManager.getString("label.load_associated_tree"));
1095 loadTreeMenuItem.setActionCommand(MessageManager
1096 .getString("label.load_tree_for_sequence_set"));
1097 loadTreeMenuItem.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 loadTreeMenuItem_actionPerformed(e);
1106 scaleAbove.setVisible(false);
1107 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1108 scaleAbove.addActionListener(new ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 scaleAbove_actionPerformed(e);
1116 scaleLeft.setVisible(false);
1117 scaleLeft.setSelected(true);
1118 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1119 scaleLeft.addActionListener(new ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 scaleLeft_actionPerformed(e);
1127 scaleRight.setVisible(false);
1128 scaleRight.setSelected(true);
1129 scaleRight.setText(MessageManager.getString("action.scale_right"));
1130 scaleRight.addActionListener(new ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 scaleRight_actionPerformed(e);
1138 centreColumnLabelsMenuItem.setVisible(true);
1139 centreColumnLabelsMenuItem.setState(false);
1140 centreColumnLabelsMenuItem.setText(MessageManager
1141 .getString("label.centre_column_labels"));
1142 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 centreColumnLabels_actionPerformed(e);
1150 followHighlightMenuItem.setVisible(true);
1151 followHighlightMenuItem.setState(true);
1152 followHighlightMenuItem.setText(MessageManager
1153 .getString("label.automatic_scrolling"));
1154 followHighlightMenuItem.addActionListener(new ActionListener()
1158 public void actionPerformed(ActionEvent e)
1160 followHighlight_actionPerformed();
1166 .setText(MessageManager.getString("action.by_tree_order"));
1167 sort.setText(MessageManager.getString("action.sort"));
1168 sort.addMenuListener(new MenuListener()
1171 public void menuSelected(MenuEvent e)
1173 buildTreeSortMenu();
1177 public void menuDeselected(MenuEvent e)
1182 public void menuCanceled(MenuEvent e)
1186 sortByAnnotScore.setText(MessageManager
1187 .getString("label.sort_by_score"));
1188 sort.add(sortByAnnotScore);
1189 sort.addMenuListener(new javax.swing.event.MenuListener()
1193 public void menuCanceled(MenuEvent e)
1198 public void menuDeselected(MenuEvent e)
1203 public void menuSelected(MenuEvent e)
1205 buildSortByAnnotationScoresMenu();
1208 sortByAnnotScore.setVisible(false);
1210 calculateTree.setText(MessageManager
1211 .getString("action.calculate_tree_pca"));
1213 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1214 padGapsMenuitem.setState(jalview.bin.Cache
1215 .getDefault("PAD_GAPS", false));
1216 padGapsMenuitem.addActionListener(new ActionListener()
1219 public void actionPerformed(ActionEvent e)
1221 padGapsMenuitem_actionPerformed(e);
1224 JMenuItem vamsasStore = new JMenuItem(
1225 MessageManager.getString("label.vamsas_store"));
1226 vamsasStore.setVisible(false);
1227 vamsasStore.addActionListener(new ActionListener()
1230 public void actionPerformed(ActionEvent e)
1232 vamsasStore_actionPerformed(e);
1235 showTranslation.setText(MessageManager
1236 .getString("label.translate_cDNA"));
1237 showTranslation.addActionListener(new ActionListener()
1240 public void actionPerformed(ActionEvent e)
1242 showTranslation_actionPerformed(e);
1245 showReverse.setText(MessageManager.getString("label.reverse"));
1246 showReverse.addActionListener(new ActionListener()
1249 public void actionPerformed(ActionEvent e)
1251 showReverse_actionPerformed(false);
1254 showReverseComplement.setText(MessageManager
1255 .getString("label.reverse_complement"));
1256 showReverseComplement.addActionListener(new ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 showReverse_actionPerformed(true);
1265 JMenuItem extractScores = new JMenuItem(
1266 MessageManager.getString("label.extract_scores"));
1267 extractScores.addActionListener(new ActionListener()
1270 public void actionPerformed(ActionEvent e)
1272 extractScores_actionPerformed(e);
1275 extractScores.setVisible(true);
1276 // JBPNote: TODO: make gui for regex based score extraction
1278 // for show products actions see AlignFrame.canShowProducts
1279 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1281 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1282 runGroovy.setToolTipText(MessageManager
1283 .getString("label.run_groovy_tip"));
1284 runGroovy.addActionListener(new ActionListener()
1287 public void actionPerformed(ActionEvent e)
1289 runGroovy_actionPerformed();
1293 JMenuItem openFeatureSettings = new JMenuItem(
1294 MessageManager.getString("action.feature_settings"));
1295 openFeatureSettings.addActionListener(new ActionListener()
1298 public void actionPerformed(ActionEvent e)
1300 featureSettings_actionPerformed(e);
1303 JMenuItem fetchSequence = new JMenuItem(
1304 MessageManager.getString("label.fetch_sequences"));
1305 fetchSequence.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 fetchSequence_actionPerformed(e);
1314 JMenuItem associatedData = new JMenuItem(
1315 MessageManager.getString("label.load_features_annotations"));
1316 associatedData.addActionListener(new ActionListener()
1319 public void actionPerformed(ActionEvent e)
1321 associatedData_actionPerformed(e);
1324 autoCalculate.setText(MessageManager
1325 .getString("label.autocalculate_consensus"));
1326 autoCalculate.setState(jalview.bin.Cache.getDefault(
1327 "AUTO_CALC_CONSENSUS", true));
1328 autoCalculate.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 autoCalculate_actionPerformed(e);
1336 sortByTree.setText(MessageManager
1337 .getString("label.sort_alignment_new_tree"));
1339 .setToolTipText("<html>"
1341 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1343 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1344 sortByTree.addActionListener(new ActionListener()
1347 public void actionPerformed(ActionEvent e)
1349 sortByTreeOption_actionPerformed(e);
1353 listenToViewSelections.setText(MessageManager
1354 .getString("label.listen_for_selections"));
1355 listenToViewSelections
1356 .setToolTipText("<html>"
1358 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1359 listenToViewSelections.setState(false);
1360 listenToViewSelections.addActionListener(new ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 listenToViewSelections_actionPerformed(e);
1369 JMenu addSequenceMenu = new JMenu(
1370 MessageManager.getString("label.add_sequences"));
1371 JMenuItem addFromFile = new JMenuItem(
1372 MessageManager.getString("label.from_file"));
1373 addFromFile.addActionListener(new ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 addFromFile_actionPerformed(e);
1381 JMenuItem addFromText = new JMenuItem(
1382 MessageManager.getString("label.from_textbox"));
1383 addFromText.addActionListener(new ActionListener()
1386 public void actionPerformed(ActionEvent e)
1388 addFromText_actionPerformed(e);
1391 JMenuItem addFromURL = new JMenuItem(
1392 MessageManager.getString("label.from_url"));
1393 addFromURL.addActionListener(new ActionListener()
1396 public void actionPerformed(ActionEvent e)
1398 addFromURL_actionPerformed(e);
1401 JMenuItem exportFeatures = new JMenuItem(
1402 MessageManager.getString("label.export_features"));
1403 exportFeatures.addActionListener(new ActionListener()
1406 public void actionPerformed(ActionEvent e)
1408 exportFeatures_actionPerformed(e);
1411 JMenuItem exportAnnotations = new JMenuItem(
1412 MessageManager.getString("label.export_annotations"));
1413 exportAnnotations.addActionListener(new ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 exportAnnotations_actionPerformed(e);
1421 statusPanel.setLayout(new GridLayout());
1422 JMenuItem showAllSeqs = new JMenuItem(
1423 MessageManager.getString("label.all_sequences"));
1424 showAllSeqs.setToolTipText(MessageManager
1425 .getString("label.toggle_sequence_visibility"));
1426 showAllSeqs.addActionListener(new ActionListener()
1429 public void actionPerformed(ActionEvent e)
1431 showAllSeqs_actionPerformed(e);
1434 JMenuItem showAllColumns = new JMenuItem(
1435 MessageManager.getString("label.all_columns"));
1436 showAllColumns.setToolTipText(MessageManager
1437 .getString("label.toggle_columns_visibility"));
1438 showAllColumns.addActionListener(new ActionListener()
1441 public void actionPerformed(ActionEvent e)
1443 showAllColumns_actionPerformed(e);
1446 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1447 JMenuItem hideSelSequences = new JMenuItem(
1448 MessageManager.getString("label.selected_sequences"));
1449 hideSelSequences.setToolTipText(MessageManager
1450 .getString("label.toggle_sequence_visibility"));
1451 hideSelSequences.addActionListener(new ActionListener()
1454 public void actionPerformed(ActionEvent e)
1456 hideSelSequences_actionPerformed(e);
1459 JMenuItem hideSelColumns = new JMenuItem(
1460 MessageManager.getString("label.selected_columns"));
1461 hideSelColumns.setToolTipText(MessageManager
1462 .getString("label.toggle_columns_visibility"));
1463 hideSelColumns.addActionListener(new ActionListener()
1466 public void actionPerformed(ActionEvent e)
1468 hideSelColumns_actionPerformed(e);
1471 JMenuItem hideAllSelection = new JMenuItem(
1472 MessageManager.getString("label.selected_region"));
1473 hideAllSelection.addActionListener(new ActionListener()
1476 public void actionPerformed(ActionEvent e)
1478 hideAllSelection_actionPerformed(e);
1481 // TODO: should be hidden if no selection exists.
1482 JMenuItem hideAllButSelection = new JMenuItem(
1483 MessageManager.getString("label.all_but_selected_region"));
1484 hideAllButSelection.addActionListener(new ActionListener()
1487 public void actionPerformed(ActionEvent e)
1489 hideAllButSelection_actionPerformed(e);
1492 JMenuItem showAllhidden = new JMenuItem(
1493 MessageManager.getString("label.all_sequences_columns"));
1494 showAllhidden.setToolTipText(MessageManager
1495 .getString("label.toggles_visibility_hidden_selected_regions"));
1496 showAllhidden.addActionListener(new ActionListener()
1499 public void actionPerformed(ActionEvent e)
1501 showAllhidden_actionPerformed(e);
1504 hiddenMarkers.setText(MessageManager
1505 .getString("action.show_hidden_markers"));
1506 hiddenMarkers.addActionListener(new ActionListener()
1509 public void actionPerformed(ActionEvent e)
1511 hiddenMarkers_actionPerformed(e);
1515 JMenuItem invertColSel = new JMenuItem(
1516 MessageManager.getString("action.invert_column_selection"));
1517 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1518 .getDefaultToolkit().getMenuShortcutKeyMask()
1519 | KeyEvent.ALT_MASK, false);
1520 al = new ActionListener()
1523 public void actionPerformed(ActionEvent e)
1525 invertColSel_actionPerformed(e);
1528 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1530 showComplementMenuItem.setVisible(false);
1531 showComplementMenuItem.addActionListener(new ActionListener()
1534 public void actionPerformed(ActionEvent e)
1536 showComplement_actionPerformed(showComplementMenuItem.getState());
1540 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1543 public void stateChanged(ChangeEvent evt)
1545 JTabbedPane pane = (JTabbedPane) evt.getSource();
1546 int sel = pane.getSelectedIndex();
1547 tabSelectionChanged(sel);
1550 tabbedPane.addMouseListener(new MouseAdapter()
1553 public void mousePressed(MouseEvent e)
1555 if (e.isPopupTrigger()) // Mac
1557 tabbedPane_mousePressed(e);
1562 public void mouseReleased(MouseEvent e)
1564 if (e.isPopupTrigger()) // Windows
1566 tabbedPane_mousePressed(e);
1570 tabbedPane.addFocusListener(new FocusAdapter()
1573 public void focusGained(FocusEvent e)
1575 tabbedPane_focusGained(e);
1579 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1580 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1581 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1582 al = new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 save_actionPerformed(e);
1590 addMenuActionAndAccelerator(keyStroke, save, al);
1592 reload.setEnabled(false);
1593 reload.setText(MessageManager.getString("action.reload"));
1594 reload.addActionListener(new ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 reload_actionPerformed(e);
1603 JMenuItem newView = new JMenuItem(
1604 MessageManager.getString("action.new_view"));
1605 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1606 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1607 al = new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 newView_actionPerformed(e);
1615 addMenuActionAndAccelerator(keyStroke, newView, al);
1617 tabbedPane.setToolTipText("<html><i>"
1618 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1621 formatMenu.setText(MessageManager.getString("action.format"));
1622 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1624 idRightAlign.setText(MessageManager
1625 .getString("label.right_align_sequence_id"));
1626 idRightAlign.addActionListener(new ActionListener()
1629 public void actionPerformed(ActionEvent e)
1631 idRightAlign_actionPerformed(e);
1635 gatherViews.setEnabled(false);
1636 gatherViews.setText(MessageManager.getString("action.gather_views"));
1637 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1638 al = new ActionListener()
1641 public void actionPerformed(ActionEvent e)
1643 gatherViews_actionPerformed(e);
1646 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1648 expandViews.setEnabled(false);
1649 expandViews.setText(MessageManager.getString("action.expand_views"));
1650 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1651 al = new ActionListener()
1654 public void actionPerformed(ActionEvent e)
1656 expandViews_actionPerformed(e);
1659 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1661 JMenuItem pageSetup = new JMenuItem(
1662 MessageManager.getString("action.page_setup"));
1663 pageSetup.addActionListener(new ActionListener()
1666 public void actionPerformed(ActionEvent e)
1668 pageSetup_actionPerformed(e);
1671 JMenuItem alignmentProperties = new JMenuItem(
1672 MessageManager.getString("label.alignment_props"));
1673 alignmentProperties.addActionListener(new ActionListener()
1676 public void actionPerformed(ActionEvent actionEvent)
1678 alignmentProperties();
1681 JMenuItem selectHighlighted = new JMenuItem(
1682 MessageManager.getString("action.select_highlighted_columns"));
1683 selectHighlighted.setToolTipText(MessageManager
1684 .getString("tooltip.select_highlighted_columns"));
1685 al = new ActionListener()
1688 public void actionPerformed(ActionEvent actionEvent)
1690 selectHighlightedColumns_actionPerformed(actionEvent);
1693 selectHighlighted.addActionListener(al);
1694 JMenu tooltipSettingsMenu = new JMenu(
1695 MessageManager.getString("label.sequence_id_tooltip"));
1696 JMenu autoAnnMenu = new JMenu(
1697 MessageManager.getString("label.autocalculated_annotation"));
1699 JMenu exportImageMenu = new JMenu(
1700 MessageManager.getString("label.export_image"));
1701 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1702 alignFrameMenuBar.add(fileMenu);
1703 alignFrameMenuBar.add(editMenu);
1704 alignFrameMenuBar.add(selectMenu);
1705 alignFrameMenuBar.add(viewMenu);
1706 alignFrameMenuBar.add(annotationsMenu);
1707 alignFrameMenuBar.add(formatMenu);
1708 alignFrameMenuBar.add(colourMenu);
1709 alignFrameMenuBar.add(calculateMenu);
1710 alignFrameMenuBar.add(webService);
1711 alignFrameMenuBar.add(hmmerMenu);
1713 fileMenu.add(fetchSequence);
1714 fileMenu.add(addSequenceMenu);
1715 fileMenu.add(reload);
1716 fileMenu.addSeparator();
1717 fileMenu.add(vamsasStore);
1719 fileMenu.add(saveAs);
1720 fileMenu.add(outputTextboxMenu);
1721 fileMenu.add(pageSetup);
1722 fileMenu.add(printMenuItem);
1723 fileMenu.addSeparator();
1724 fileMenu.add(exportImageMenu);
1725 fileMenu.add(exportFeatures);
1726 fileMenu.add(exportAnnotations);
1727 fileMenu.add(loadTreeMenuItem);
1728 fileMenu.add(associatedData);
1729 fileMenu.addSeparator();
1730 fileMenu.add(closeMenuItem);
1732 pasteMenu.add(pasteNew);
1733 pasteMenu.add(pasteThis);
1734 editMenu.add(undoMenuItem);
1735 editMenu.add(redoMenuItem);
1738 editMenu.add(pasteMenu);
1739 editMenu.add(delete);
1740 editMenu.addSeparator();
1741 editMenu.add(remove2LeftMenuItem);
1742 editMenu.add(remove2RightMenuItem);
1743 editMenu.add(removeGappedColumnMenuItem);
1744 editMenu.add(removeAllGapsMenuItem);
1745 editMenu.add(removeRedundancyMenuItem);
1746 editMenu.addSeparator();
1747 // dont add these yet in the CVS build - they cannot be undone!
1748 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1749 // editMenu.add(justifyLeftMenuItem);
1750 // editMenu.add(justifyRightMenuItem);
1751 // editMenu.addSeparator();
1752 editMenu.add(padGapsMenuitem);
1754 showMenu.add(showAllColumns);
1755 showMenu.add(showAllSeqs);
1756 showMenu.add(showAllhidden);
1757 hideMenu.add(hideSelColumns);
1758 hideMenu.add(hideSelSequences);
1759 hideMenu.add(hideAllSelection);
1760 hideMenu.add(hideAllButSelection);
1761 viewMenu.add(newView);
1762 viewMenu.add(expandViews);
1763 viewMenu.add(gatherViews);
1764 viewMenu.addSeparator();
1765 viewMenu.add(showMenu);
1766 viewMenu.add(hideMenu);
1767 viewMenu.add(showComplementMenuItem);
1768 viewMenu.addSeparator();
1769 viewMenu.add(followHighlightMenuItem);
1770 viewMenu.addSeparator();
1771 viewMenu.add(showSeqFeatures);
1772 // viewMenu.add(showSeqFeaturesHeight);
1773 viewMenu.add(openFeatureSettings);
1774 tooltipSettingsMenu.add(showDbRefsMenuitem);
1775 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1776 viewMenu.add(tooltipSettingsMenu);
1777 viewMenu.addSeparator();
1778 viewMenu.add(alignmentProperties);
1779 viewMenu.addSeparator();
1780 viewMenu.add(overviewMenuItem);
1782 annotationsMenu.add(annotationPanelMenuItem);
1783 annotationsMenu.addSeparator();
1784 annotationsMenu.add(showAllAlAnnotations);
1785 annotationsMenu.add(hideAllAlAnnotations);
1786 annotationsMenu.addSeparator();
1787 annotationsMenu.add(showAllSeqAnnotations);
1788 annotationsMenu.add(hideAllSeqAnnotations);
1789 annotationsMenu.add(sortAnnBySequence);
1790 annotationsMenu.add(sortAnnByLabel);
1791 annotationsMenu.addSeparator();
1792 autoAnnMenu.add(showAutoFirst);
1793 autoAnnMenu.add(showAutoLast);
1794 autoAnnMenu.addSeparator();
1795 autoAnnMenu.add(applyAutoAnnotationSettings);
1796 autoAnnMenu.add(showConsensusHistogram);
1797 autoAnnMenu.add(showSequenceLogo);
1798 autoAnnMenu.add(normaliseSequenceLogo);
1799 autoAnnMenu.addSeparator();
1800 autoAnnMenu.add(showGroupConservation);
1801 autoAnnMenu.add(showGroupConsensus);
1802 annotationsMenu.add(autoAnnMenu);
1805 sort.add(sortIDMenuItem);
1806 sort.add(sortLengthMenuItem);
1807 sort.add(sortGroupMenuItem);
1808 sort.add(sortPairwiseMenuItem);
1809 sort.add(sortByTreeMenu);
1810 calculateMenu.add(sort);
1811 calculateMenu.add(calculateTree);
1812 calculateMenu.addSeparator();
1813 calculateMenu.add(pairwiseAlignmentMenuItem);
1814 calculateMenu.addSeparator();
1815 calculateMenu.add(showTranslation);
1816 calculateMenu.add(showReverse);
1817 calculateMenu.add(showReverseComplement);
1818 calculateMenu.add(showProducts);
1819 calculateMenu.add(autoCalculate);
1820 calculateMenu.add(sortByTree);
1821 calculateMenu.addSeparator();
1822 calculateMenu.add(expandAlignment);
1823 calculateMenu.add(extractScores);
1824 calculateMenu.addSeparator();
1825 calculateMenu.add(runGroovy);
1827 webServiceNoServices = new JMenuItem(
1828 MessageManager.getString("label.no_services"));
1829 webService.add(webServiceNoServices);
1830 exportImageMenu.add(htmlMenuItem);
1831 exportImageMenu.add(epsFile);
1832 exportImageMenu.add(createPNG);
1833 exportImageMenu.add(createBioJS);
1834 exportImageMenu.add(createSVG);
1835 addSequenceMenu.add(addFromFile);
1836 addSequenceMenu.add(addFromText);
1837 addSequenceMenu.add(addFromURL);
1838 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1839 statusPanel.add(statusBar, null);
1840 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1842 formatMenu.add(font);
1843 formatMenu.addSeparator();
1844 formatMenu.add(wrapMenuItem);
1845 formatMenu.add(scaleAbove);
1846 formatMenu.add(scaleLeft);
1847 formatMenu.add(scaleRight);
1848 formatMenu.add(seqLimits);
1849 formatMenu.add(idRightAlign);
1850 formatMenu.add(hiddenMarkers);
1851 formatMenu.add(viewBoxesMenuItem);
1852 formatMenu.add(viewTextMenuItem);
1853 formatMenu.add(colourTextMenuItem);
1854 formatMenu.add(renderGapsMenuItem);
1855 formatMenu.add(centreColumnLabelsMenuItem);
1856 formatMenu.add(showNonconservedMenuItem);
1857 selectMenu.add(findMenuItem);
1858 selectMenu.addSeparator();
1859 selectMenu.add(selectAllSequenceMenuItem);
1860 selectMenu.add(deselectAllSequenceMenuItem);
1861 selectMenu.add(invertSequenceMenuItem);
1862 selectMenu.add(invertColSel);
1863 selectMenu.add(createGroup);
1864 selectMenu.add(unGroup);
1865 selectMenu.add(grpsFromSelection);
1866 selectMenu.add(deleteGroups);
1867 selectMenu.add(annotationColumn);
1868 selectMenu.add(selectHighlighted);
1869 // TODO - determine if the listenToViewSelections button is needed : see bug
1871 // selectMenu.addSeparator();
1872 // selectMenu.add(listenToViewSelections);
1876 * Constructs the entries on the Colour menu (but does not add them to the
1879 protected void initHMMERMenu()
1881 autoAlignSeqs = new JCheckBoxMenuItem(
1882 MessageManager.getString("label.auto_align_seqs"));
1883 hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
1884 hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
1885 hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
1886 autoAlignSeqs.addActionListener(new ActionListener()
1889 public void actionPerformed(ActionEvent e)
1891 autoAlignSeqs_actionPerformed(autoAlignSeqs.isSelected());
1896 protected void initColourMenu()
1898 applyToAllGroups = new JCheckBoxMenuItem(
1899 MessageManager.getString("label.apply_colour_to_all_groups"));
1900 applyToAllGroups.addActionListener(new ActionListener()
1903 public void actionPerformed(ActionEvent e)
1905 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1909 textColour = new JMenuItem(
1910 MessageManager.getString("label.text_colour"));
1911 textColour.addActionListener(new ActionListener()
1914 public void actionPerformed(ActionEvent e)
1916 textColour_actionPerformed();
1920 conservationMenuItem = new JCheckBoxMenuItem(
1921 MessageManager.getString("action.by_conservation"));
1922 conservationMenuItem.addActionListener(new ActionListener()
1925 public void actionPerformed(ActionEvent e)
1927 conservationMenuItem_actionPerformed(conservationMenuItem
1932 abovePIDThreshold = new JCheckBoxMenuItem(
1933 MessageManager.getString("label.above_identity_threshold"));
1934 abovePIDThreshold.addActionListener(new ActionListener()
1937 public void actionPerformed(ActionEvent e)
1939 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1942 modifyPID = new JMenuItem(
1943 MessageManager.getString("label.modify_identity_threshold"));
1944 modifyPID.addActionListener(new ActionListener()
1947 public void actionPerformed(ActionEvent e)
1949 modifyPID_actionPerformed();
1952 modifyConservation = new JMenuItem(
1954 .getString("label.modify_conservation_threshold"));
1955 modifyConservation.addActionListener(new ActionListener()
1958 public void actionPerformed(ActionEvent e)
1960 modifyConservation_actionPerformed();
1964 annotationColour = new JMenuItem(
1965 MessageManager.getString("action.by_annotation"));
1966 annotationColour.addActionListener(new ActionListener()
1969 public void actionPerformed(ActionEvent e)
1971 annotationColour_actionPerformed();
1976 protected void selectHighlightedColumns_actionPerformed(
1977 ActionEvent actionEvent)
1979 // TODO Auto-generated method stub
1984 * Generate the reverse sequence (or reverse complement if the flag is true)
1985 * and add it to the alignment
1989 protected void showReverse_actionPerformed(boolean complement)
1994 * Try to run script in a Groovy console, having first ensured that this
1995 * alignframe is set as currentAlignFrame in Desktop
1997 protected void runGroovy_actionPerformed()
2003 * Adds the given action listener and key accelerator to the given menu item.
2004 * Also saves in a lookup table to support lookup of action by key stroke.
2008 * @param actionListener
2010 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2011 JMenuItem menuItem, ActionListener actionListener)
2013 menuItem.setAccelerator(keyStroke);
2014 accelerators.put(keyStroke, menuItem);
2015 menuItem.addActionListener(actionListener);
2019 * Action on clicking sort annotations by type.
2023 protected void sortAnnotations_actionPerformed()
2028 * Action on clicking Show all annotations.
2030 * @param forSequences
2031 * update sequence-related annotations
2032 * @param forAlignment
2033 * update non-sequence-related annotations
2035 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2036 boolean forAlignment)
2038 setAnnotationsVisibility(true, forSequences, forAlignment);
2042 * Action on clicking Hide all annotations.
2044 * @param forSequences
2045 * update sequence-related annotations
2046 * @param forAlignment
2047 * update non-sequence-related annotations
2049 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2050 boolean forAlignment)
2052 setAnnotationsVisibility(false, forSequences, forAlignment);
2056 * Set the visibility of annotations to true or false. Can act on
2057 * sequence-related annotations, or alignment-related, or both.
2060 * @param forSequences
2061 * update sequence-related annotations
2062 * @param forAlignment
2063 * update non-sequence-related annotations
2065 protected void setAnnotationsVisibility(boolean visible,
2066 boolean forSequences, boolean forAlignment)
2071 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2073 // TODO Auto-generated method stub
2077 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2079 // TODO Auto-generated method stub
2083 protected void showAllhidden_actionPerformed(ActionEvent e)
2085 // TODO Auto-generated method stub
2089 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2091 // TODO Auto-generated method stub
2095 protected void hideAllSelection_actionPerformed(ActionEvent e)
2097 // TODO Auto-generated method stub
2101 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2103 // TODO Auto-generated method stub
2107 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2109 // TODO Auto-generated method stub
2113 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2115 // TODO Auto-generated method stub
2119 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2121 // TODO Auto-generated method stub
2125 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2127 // TODO Auto-generated method stub
2131 protected void showGroupConservation_actionPerformed(ActionEvent e)
2133 // TODO Auto-generated method stub
2137 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2139 // TODO Auto-generated method stub
2143 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2145 // TODO Auto-generated method stub
2149 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2151 // TODO Auto-generated method stub
2155 protected void followHighlight_actionPerformed()
2157 // TODO Auto-generated method stub
2161 protected void showNpFeats_actionPerformed(ActionEvent e)
2163 // TODO Auto-generated method stub
2167 protected void showDbRefs_actionPerformed(ActionEvent e)
2169 // TODO Auto-generated method stub
2173 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2177 protected void buildSortByAnnotationScoresMenu()
2181 protected void extractScores_actionPerformed(ActionEvent e)
2185 protected void outputText_actionPerformed(ActionEvent e)
2189 public void addFromFile_actionPerformed(ActionEvent e)
2194 public void addFromText_actionPerformed(ActionEvent e)
2199 public void addFromURL_actionPerformed(ActionEvent e)
2204 public void exportFeatures_actionPerformed(ActionEvent e)
2209 public void exportAnnotations_actionPerformed(ActionEvent e)
2214 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2218 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2223 protected void closeMenuItem_actionPerformed(boolean b)
2227 protected void redoMenuItem_actionPerformed(ActionEvent e)
2231 protected void undoMenuItem_actionPerformed(ActionEvent e)
2235 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2239 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2243 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2247 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2251 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2255 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2259 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2263 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2267 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2271 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2275 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2279 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2283 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2287 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2291 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2295 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2299 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2303 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2307 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2311 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2315 protected void conservationMenuItem_actionPerformed(boolean selected)
2319 protected void printMenuItem_actionPerformed(ActionEvent e)
2323 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2327 protected void findMenuItem_actionPerformed(ActionEvent e)
2331 protected void abovePIDThreshold_actionPerformed(boolean selected)
2335 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2339 protected void deleteGroups_actionPerformed(ActionEvent e)
2343 protected void createGroup_actionPerformed(ActionEvent e)
2347 protected void unGroup_actionPerformed(ActionEvent e)
2351 protected void copy_actionPerformed(ActionEvent e)
2355 protected void cut_actionPerformed(ActionEvent e)
2359 protected void delete_actionPerformed(ActionEvent e)
2363 protected void pasteNew_actionPerformed(ActionEvent e)
2367 protected void pasteThis_actionPerformed(ActionEvent e)
2371 protected void applyToAllGroups_actionPerformed(boolean selected)
2375 protected void autoAlignSeqs_actionPerformed(boolean selected)
2379 protected void hmmAlign_actionPerformed(ActionEvent e)
2383 protected void hmmBuild_actionPerformed(ActionEvent e)
2387 protected void hmmSearch_actionPerformed(ActionEvent e)
2391 public void createPNG(java.io.File f)
2395 protected void font_actionPerformed(ActionEvent e)
2399 protected void seqLimit_actionPerformed(ActionEvent e)
2403 public void seqDBRef_actionPerformed(ActionEvent e)
2408 public void createEPS(java.io.File f)
2412 public void createSVG(java.io.File f)
2417 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2423 * Template method to handle the 'load T-Coffee scores' menu event.
2425 * Subclasses override this method to provide a custom action.
2430 protected void loadScores_actionPerformed(ActionEvent event)
2435 protected void jpred_actionPerformed(ActionEvent e)
2439 protected void scaleAbove_actionPerformed(ActionEvent e)
2443 protected void scaleLeft_actionPerformed(ActionEvent e)
2447 protected void scaleRight_actionPerformed(ActionEvent e)
2451 protected void modifyPID_actionPerformed()
2455 protected void modifyConservation_actionPerformed()
2459 protected void saveAs_actionPerformed(ActionEvent e)
2463 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2467 public void vamsasStore_actionPerformed(ActionEvent e)
2472 public void vamsasLoad_actionPerformed(ActionEvent e)
2477 public void showTranslation_actionPerformed(ActionEvent e)
2482 public void featureSettings_actionPerformed(ActionEvent e)
2487 public void fetchSequence_actionPerformed(ActionEvent e)
2492 public void smoothFont_actionPerformed(ActionEvent e)
2497 public void annotationColour_actionPerformed()
2501 public void annotationColumn_actionPerformed(ActionEvent e)
2505 public void associatedData_actionPerformed(ActionEvent e)
2510 public void autoCalculate_actionPerformed(ActionEvent e)
2515 public void sortByTreeOption_actionPerformed(ActionEvent e)
2520 public void showAllSeqs_actionPerformed(ActionEvent e)
2525 public void showAllColumns_actionPerformed(ActionEvent e)
2530 public void hideSelSequences_actionPerformed(ActionEvent e)
2535 public void hideSelColumns_actionPerformed(ActionEvent e)
2540 public void hiddenMarkers_actionPerformed(ActionEvent e)
2545 public void findPdbId_actionPerformed(ActionEvent e)
2550 public void enterPdbId_actionPerformed(ActionEvent e)
2555 public void pdbFile_actionPerformed(ActionEvent e)
2560 public void invertColSel_actionPerformed(ActionEvent e)
2565 public void tabSelectionChanged(int sel)
2570 public void tabbedPane_mousePressed(MouseEvent e)
2575 public void tabbedPane_focusGained(FocusEvent e)
2580 public void save_actionPerformed(ActionEvent e)
2585 public void reload_actionPerformed(ActionEvent e)
2590 public void newView_actionPerformed(ActionEvent e)
2595 public void textColour_actionPerformed()
2600 public void idRightAlign_actionPerformed(ActionEvent e)
2605 public void expandViews_actionPerformed(ActionEvent e)
2610 public void gatherViews_actionPerformed(ActionEvent e)
2615 public void buildTreeSortMenu()
2620 public void pageSetup_actionPerformed(ActionEvent e)
2625 public void alignmentProperties()
2630 protected void expand_newalign(ActionEvent e)
2632 // TODO Auto-generated method stub
2636 protected boolean isShowAutoCalculatedAbove()
2638 return showAutoCalculatedAbove;
2641 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2643 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2646 protected SequenceAnnotationOrder getAnnotationSortOrder()
2648 return annotationSortOrder;
2651 protected void setAnnotationSortOrder(
2652 SequenceAnnotationOrder annotationSortOrder)
2654 this.annotationSortOrder = annotationSortOrder;
2657 public Map<KeyStroke, JMenuItem> getAccelerators()
2659 return this.accelerators;
2663 * Returns the selected index of the tabbed pane, or -1 if none selected
2664 * (including the case where the tabbed pane has not been made visible).
2668 public int getTabIndex()
2670 return tabbedPane.getSelectedIndex();
2673 public JPanel getStatusPanel()
2679 * Sets a reference to the containing split frame. Also makes the 'toggle
2680 * split view' menu item visible and checked.
2684 public void setSplitFrame(SplitContainerI sf)
2686 this.splitFrame = sf;
2689 this.showComplementMenuItem.setVisible(true);
2690 this.showComplementMenuItem.setState(true);
2694 public SplitContainerI getSplitViewContainer()
2696 return this.splitFrame;
2699 protected void showComplement_actionPerformed(boolean complement)
2703 protected void showInformationHistogram_actionPerformed(ActionEvent e)
2705 // TODO Auto-generated method stub
2709 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2711 // TODO Auto-generated method stub
2715 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2717 // TODO Auto-generated method stub