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.io.IOException;
44 import java.util.HashMap;
47 import javax.swing.BorderFactory;
48 import javax.swing.ButtonGroup;
49 import javax.swing.JCheckBoxMenuItem;
50 import javax.swing.JInternalFrame;
51 import javax.swing.JLabel;
52 import javax.swing.JMenu;
53 import javax.swing.JMenuBar;
54 import javax.swing.JMenuItem;
55 import javax.swing.JPanel;
56 import javax.swing.JRadioButtonMenuItem;
57 import javax.swing.JTabbedPane;
58 import javax.swing.KeyStroke;
59 import javax.swing.event.ChangeEvent;
60 import javax.swing.event.MenuEvent;
61 import javax.swing.event.MenuListener;
63 public class GAlignFrame extends JInternalFrame
65 protected JMenuBar alignFrameMenuBar = new JMenuBar();
67 protected JMenuItem closeMenuItem = new JMenuItem();
69 protected JMenu webService = new JMenu();
71 protected JMenu hmmerMenu = new JMenu();
73 protected JCheckBoxMenuItem autoAlignSeqs = new JCheckBoxMenuItem();
75 protected JMenuItem hmmAlign = new JMenuItem();
77 protected JMenuItem hmmSearch = new JMenuItem();
79 protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
81 protected JMenuItem webServiceNoServices;
83 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
85 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
87 protected JMenu sortByAnnotScore = new JMenu();
89 public JLabel statusBar = new JLabel();
91 protected JMenu outputTextboxMenu = new JMenu();
93 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
95 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
97 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
99 protected JMenuItem undoMenuItem = new JMenuItem();
101 protected JMenuItem redoMenuItem = new JMenuItem();
103 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
105 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
107 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
109 JMenuItem copy = new JMenuItem();
111 JMenuItem cut = new JMenuItem();
113 JMenu pasteMenu = new JMenu();
115 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
117 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
119 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
121 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
123 protected JCheckBoxMenuItem applyToAllGroups;
125 protected JMenu colourMenu = new JMenu();
127 protected JMenuItem textColour;
129 protected JCheckBoxMenuItem conservationMenuItem;
131 protected JMenuItem modifyConservation;
133 protected JCheckBoxMenuItem abovePIDThreshold;
135 protected JMenuItem modifyPID;
137 protected JMenuItem annotationColour;
139 protected JMenu sortByTreeMenu = new JMenu();
141 protected JMenu sort = new JMenu();
143 protected JMenuItem calculateTree = new JMenuItem();
145 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
147 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
149 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
151 protected JMenuItem showTranslation = new JMenuItem();
153 protected JMenuItem showReverse = new JMenuItem();
155 protected JMenuItem showReverseComplement = new JMenuItem();
157 protected JMenu showProducts = new JMenu();
159 protected JMenuItem runGroovy = new JMenuItem();
161 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
163 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
165 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
167 protected JPanel statusPanel = new JPanel();
169 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
171 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
173 protected JMenuItem showAllAlAnnotations = new JMenuItem();
175 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
177 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
179 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
181 protected JTabbedPane tabbedPane = new JTabbedPane();
183 protected JMenuItem reload = new JMenuItem();
185 protected JMenu formatMenu = new JMenu();
187 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
189 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
191 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
193 protected JMenuItem gatherViews = new JMenuItem();
195 protected JMenuItem expandViews = new JMenuItem();
197 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
203 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
209 protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
211 protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
213 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
215 private SequenceAnnotationOrder annotationSortOrder;
217 private boolean showAutoCalculatedAbove = false;
219 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
221 private SplitContainerI splitFrame;
228 setJMenuBar(alignFrameMenuBar);
230 // dynamically fill save as menu with available formats
231 for (String ff : FileFormats.getInstance().getWritableFormats(true))
233 JMenuItem item = new JMenuItem(ff);
235 item.addActionListener(new ActionListener()
238 public void actionPerformed(ActionEvent e)
240 outputText_actionPerformed(e);
244 outputTextboxMenu.add(item);
246 } catch (Exception e)
248 System.err.println(e.toString());
251 if (!Platform.isAMac())
253 closeMenuItem.setMnemonic('C');
254 outputTextboxMenu.setMnemonic('T');
255 undoMenuItem.setMnemonic('Z');
256 redoMenuItem.setMnemonic('0');
257 copy.setMnemonic('C');
258 cut.setMnemonic('U');
259 pasteMenu.setMnemonic('P');
260 reload.setMnemonic('R');
264 private void jbInit() throws Exception
269 JMenuItem saveAs = new JMenuItem(
270 MessageManager.getString("action.save_as"));
271 ActionListener al = new ActionListener()
274 public void actionPerformed(ActionEvent e)
276 saveAs_actionPerformed(e);
280 // FIXME getDefaultToolkit throws an exception in Headless mode
281 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
282 .getDefaultToolkit().getMenuShortcutKeyMask()
283 | KeyEvent.SHIFT_MASK, false);
284 addMenuActionAndAccelerator(keyStroke, saveAs, al);
286 closeMenuItem.setText(MessageManager.getString("action.close"));
287 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
288 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
289 al = new ActionListener()
292 public void actionPerformed(ActionEvent e)
294 closeMenuItem_actionPerformed(false);
297 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
299 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
300 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
301 JMenu annotationsMenu = new JMenu(
302 MessageManager.getString("action.annotations"));
303 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
304 colourMenu.setText(MessageManager.getString("action.colour"));
305 JMenu calculateMenu = new JMenu(
306 MessageManager.getString("action.calculate"));
307 webService.setText(MessageManager.getString("action.web_service"));
308 hmmerMenu.setText(MessageManager.getString("action.hmmer"));
309 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
310 MessageManager.getString("action.select_all"));
311 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
312 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
313 al = new ActionListener()
316 public void actionPerformed(ActionEvent e)
318 selectAllSequenceMenuItem_actionPerformed(e);
321 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
323 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
324 MessageManager.getString("action.deselect_all"));
325 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
326 al = new ActionListener()
329 public void actionPerformed(ActionEvent e)
331 deselectAllSequenceMenuItem_actionPerformed(e);
334 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
336 JMenuItem invertSequenceMenuItem = new JMenuItem(
337 MessageManager.getString("action.invert_sequence_selection"));
338 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
339 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
340 al = new ActionListener()
343 public void actionPerformed(ActionEvent e)
345 invertSequenceMenuItem_actionPerformed(e);
348 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
350 JMenuItem grpsFromSelection = new JMenuItem(
351 MessageManager.getString("action.make_groups_selection"));
352 grpsFromSelection.addActionListener(new ActionListener()
355 public void actionPerformed(ActionEvent e)
357 makeGrpsFromSelection_actionPerformed(e);
360 JMenuItem expandAlignment = new JMenuItem(
361 MessageManager.getString("action.view_flanking_regions"));
362 expandAlignment.setToolTipText(MessageManager
363 .getString("label.view_flanking_regions"));
364 expandAlignment.addActionListener(new ActionListener()
367 public void actionPerformed(ActionEvent e)
372 JMenuItem remove2LeftMenuItem = new JMenuItem(
373 MessageManager.getString("action.remove_left"));
374 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
375 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
376 al = new ActionListener()
379 public void actionPerformed(ActionEvent e)
381 remove2LeftMenuItem_actionPerformed(e);
384 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
386 JMenuItem remove2RightMenuItem = new JMenuItem(
387 MessageManager.getString("action.remove_right"));
388 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
389 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
390 al = new ActionListener()
393 public void actionPerformed(ActionEvent e)
395 remove2RightMenuItem_actionPerformed(e);
398 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
400 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
401 MessageManager.getString("action.remove_empty_columns"));
402 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
403 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
404 al = new ActionListener()
407 public void actionPerformed(ActionEvent e)
409 removeGappedColumnMenuItem_actionPerformed(e);
412 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
414 JMenuItem removeAllGapsMenuItem = new JMenuItem(
415 MessageManager.getString("action.remove_all_gaps"));
416 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
417 .getDefaultToolkit().getMenuShortcutKeyMask()
418 | KeyEvent.SHIFT_MASK, false);
419 al = new ActionListener()
422 public void actionPerformed(ActionEvent e)
424 removeAllGapsMenuItem_actionPerformed(e);
427 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
429 JMenuItem justifyLeftMenuItem = new JMenuItem(
430 MessageManager.getString("action.left_justify_alignment"));
431 justifyLeftMenuItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent e)
436 justifyLeftMenuItem_actionPerformed(e);
439 JMenuItem justifyRightMenuItem = new JMenuItem(
440 MessageManager.getString("action.right_justify_alignment"));
441 justifyRightMenuItem.addActionListener(new ActionListener()
444 public void actionPerformed(ActionEvent e)
446 justifyRightMenuItem_actionPerformed(e);
449 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
450 viewBoxesMenuItem.setState(true);
451 viewBoxesMenuItem.addActionListener(new ActionListener()
454 public void actionPerformed(ActionEvent e)
456 viewBoxesMenuItem_actionPerformed(e);
459 viewTextMenuItem.setText(MessageManager.getString("action.text"));
460 viewTextMenuItem.setState(true);
461 viewTextMenuItem.addActionListener(new ActionListener()
464 public void actionPerformed(ActionEvent e)
466 viewTextMenuItem_actionPerformed(e);
469 showNonconservedMenuItem.setText(MessageManager
470 .getString("label.show_non_conserved"));
471 showNonconservedMenuItem.setState(false);
472 showNonconservedMenuItem.addActionListener(new ActionListener()
475 public void actionPerformed(ActionEvent e)
477 showUnconservedMenuItem_actionPerformed(e);
480 JMenuItem sortPairwiseMenuItem = new JMenuItem(
481 MessageManager.getString("action.by_pairwise_id"));
482 sortPairwiseMenuItem.addActionListener(new ActionListener()
485 public void actionPerformed(ActionEvent e)
487 sortPairwiseMenuItem_actionPerformed(e);
490 JMenuItem sortIDMenuItem = new JMenuItem(
491 MessageManager.getString("action.by_id"));
492 sortIDMenuItem.addActionListener(new ActionListener()
495 public void actionPerformed(ActionEvent e)
497 sortIDMenuItem_actionPerformed(e);
500 JMenuItem sortLengthMenuItem = new JMenuItem(
501 MessageManager.getString("action.by_length"));
502 sortLengthMenuItem.addActionListener(new ActionListener()
505 public void actionPerformed(ActionEvent e)
507 sortLengthMenuItem_actionPerformed(e);
510 JMenuItem sortGroupMenuItem = new JMenuItem(
511 MessageManager.getString("action.by_group"));
512 sortGroupMenuItem.addActionListener(new ActionListener()
515 public void actionPerformed(ActionEvent e)
517 sortGroupMenuItem_actionPerformed(e);
521 JMenuItem removeRedundancyMenuItem = new JMenuItem(
522 MessageManager.getString("action.remove_redundancy"));
523 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
524 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
525 al = new ActionListener()
528 public void actionPerformed(ActionEvent e)
530 removeRedundancyMenuItem_actionPerformed(e);
533 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
535 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
536 MessageManager.getString("action.pairwise_alignment"));
537 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
540 public void actionPerformed(ActionEvent e)
542 pairwiseAlignmentMenuItem_actionPerformed(e);
546 this.getContentPane().setLayout(new BorderLayout());
547 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
548 statusBar.setBackground(Color.white);
549 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
550 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
551 statusBar.setText(MessageManager.getString("label.status_bar"));
552 outputTextboxMenu.setText(MessageManager
553 .getString("label.out_to_textbox"));
555 annotationPanelMenuItem.setActionCommand("");
556 annotationPanelMenuItem.setText(MessageManager
557 .getString("label.show_annotations"));
558 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
560 annotationPanelMenuItem.addActionListener(new ActionListener()
563 public void actionPerformed(ActionEvent e)
565 annotationPanelMenuItem_actionPerformed(e);
568 showAllAlAnnotations.setText(MessageManager
569 .getString("label.show_all_al_annotations"));
570 final boolean isAnnotationPanelShown = annotationPanelMenuItem
572 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
573 showAllAlAnnotations.addActionListener(new ActionListener()
576 public void actionPerformed(ActionEvent e)
578 showAllAnnotations_actionPerformed(false, true);
581 hideAllAlAnnotations.setText(MessageManager
582 .getString("label.hide_all_al_annotations"));
583 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
584 hideAllAlAnnotations.addActionListener(new ActionListener()
587 public void actionPerformed(ActionEvent e)
589 hideAllAnnotations_actionPerformed(false, true);
592 showAllSeqAnnotations.setText(MessageManager
593 .getString("label.show_all_seq_annotations"));
594 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
595 showAllSeqAnnotations.addActionListener(new ActionListener()
598 public void actionPerformed(ActionEvent e)
600 showAllAnnotations_actionPerformed(true, false);
603 hideAllSeqAnnotations.setText(MessageManager
604 .getString("label.hide_all_seq_annotations"));
605 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
606 hideAllSeqAnnotations.addActionListener(new ActionListener()
609 public void actionPerformed(ActionEvent e)
611 hideAllAnnotations_actionPerformed(true, false);
614 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
615 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
616 SequenceAnnotationOrder.NONE.name()));
617 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
618 MessageManager.getString("label.sort_annotations_by_sequence"));
619 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
620 MessageManager.getString("label.sort_annotations_by_label"));
623 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
624 sortAnnBySequence.addActionListener(new ActionListener()
627 public void actionPerformed(ActionEvent e)
629 boolean newState = sortAnnBySequence.getState();
630 sortAnnByLabel.setSelected(false);
631 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
632 : SequenceAnnotationOrder.NONE);
633 sortAnnotations_actionPerformed();
637 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
638 sortAnnByLabel.addActionListener(new ActionListener()
641 public void actionPerformed(ActionEvent e)
643 boolean newState = sortAnnByLabel.getState();
644 sortAnnBySequence.setSelected(false);
645 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
646 : SequenceAnnotationOrder.NONE);
647 sortAnnotations_actionPerformed();
650 colourTextMenuItem = new JCheckBoxMenuItem(
652 .getString("label.colour_text"));
653 colourTextMenuItem.addActionListener(new ActionListener()
656 public void actionPerformed(ActionEvent e)
658 colourTextMenuItem_actionPerformed(e);
662 JMenuItem htmlMenuItem = new JMenuItem(
663 MessageManager.getString("label.html"));
664 htmlMenuItem.addActionListener(new ActionListener()
667 public void actionPerformed(ActionEvent e)
669 htmlMenuItem_actionPerformed(e);
673 JMenuItem createBioJS = new JMenuItem(
674 MessageManager.getString("label.biojs_html_export"));
675 createBioJS.addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 bioJSMenuItem_actionPerformed(e);
684 JMenuItem overviewMenuItem = new JMenuItem(
685 MessageManager.getString("label.overview_window"));
686 overviewMenuItem.addActionListener(new ActionListener()
689 public void actionPerformed(ActionEvent e)
691 overviewMenuItem_actionPerformed(e);
695 undoMenuItem.setEnabled(false);
696 undoMenuItem.setText(MessageManager.getString("action.undo"));
697 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
698 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
699 al = new ActionListener()
702 public void actionPerformed(ActionEvent e)
704 undoMenuItem_actionPerformed(e);
707 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
709 redoMenuItem.setEnabled(false);
710 redoMenuItem.setText(MessageManager.getString("action.redo"));
711 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
712 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
713 al = new ActionListener()
716 public void actionPerformed(ActionEvent e)
718 redoMenuItem_actionPerformed(e);
721 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
723 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
724 wrapMenuItem.addActionListener(new ActionListener()
727 public void actionPerformed(ActionEvent e)
729 wrapMenuItem_actionPerformed(e);
733 JMenuItem printMenuItem = new JMenuItem(
734 MessageManager.getString("action.print"));
735 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
736 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
737 al = new ActionListener()
740 public void actionPerformed(ActionEvent e)
742 printMenuItem_actionPerformed(e);
745 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
748 .setText(MessageManager.getString("action.show_gaps"));
749 renderGapsMenuItem.setState(true);
750 renderGapsMenuItem.addActionListener(new ActionListener()
753 public void actionPerformed(ActionEvent e)
755 renderGapsMenuItem_actionPerformed(e);
759 JMenuItem findMenuItem = new JMenuItem(
760 MessageManager.getString("action.find"));
761 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
762 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
763 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
764 MessageManager.getString("label.find_tip")));
765 al = new ActionListener()
768 public void actionPerformed(ActionEvent e)
770 findMenuItem_actionPerformed(e);
773 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
775 showSeqFeatures.setText(MessageManager
776 .getString("label.show_sequence_features"));
777 showSeqFeatures.addActionListener(new ActionListener()
780 public void actionPerformed(ActionEvent actionEvent)
782 showSeqFeatures_actionPerformed(actionEvent);
786 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
787 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
788 * void actionPerformed(ActionEvent actionEvent) {
789 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
791 showDbRefsMenuitem.setText(MessageManager
792 .getString("label.show_database_refs"));
793 showDbRefsMenuitem.addActionListener(new ActionListener()
797 public void actionPerformed(ActionEvent e)
799 showDbRefs_actionPerformed(e);
803 showNpFeatsMenuitem.setText(MessageManager
804 .getString("label.show_non_positional_features"));
805 showNpFeatsMenuitem.addActionListener(new ActionListener()
809 public void actionPerformed(ActionEvent e)
811 showNpFeats_actionPerformed(e);
815 showGroupConservation.setText(MessageManager
816 .getString("label.group_conservation"));
817 showGroupConservation.addActionListener(new ActionListener()
821 public void actionPerformed(ActionEvent e)
823 showGroupConservation_actionPerformed(e);
828 showGroupConsensus.setText(MessageManager
829 .getString("label.group_consensus"));
830 showGroupConsensus.addActionListener(new ActionListener()
834 public void actionPerformed(ActionEvent e)
836 showGroupConsensus_actionPerformed(e);
840 showConsensusHistogram.setText(MessageManager
841 .getString("label.show_consensus_histogram"));
842 showConsensusHistogram.addActionListener(new ActionListener()
846 public void actionPerformed(ActionEvent e)
848 showConsensusHistogram_actionPerformed(e);
852 showSequenceLogo.setText(MessageManager
853 .getString("label.show_consensus_logo"));
854 showSequenceLogo.addActionListener(new ActionListener()
858 public void actionPerformed(ActionEvent e)
860 showSequenceLogo_actionPerformed(e);
864 normaliseSequenceLogo.setText(MessageManager
865 .getString("label.norm_consensus_logo"));
866 normaliseSequenceLogo.addActionListener(new ActionListener()
870 public void actionPerformed(ActionEvent e)
872 normaliseSequenceLogo_actionPerformed(e);
876 applyAutoAnnotationSettings.setText(MessageManager
877 .getString("label.apply_all_groups"));
878 applyAutoAnnotationSettings.setState(false);
879 applyAutoAnnotationSettings.setVisible(true);
880 applyAutoAnnotationSettings.addActionListener(new ActionListener()
883 public void actionPerformed(ActionEvent e)
885 applyAutoAnnotationSettings_actionPerformed(e);
889 ButtonGroup buttonGroup = new ButtonGroup();
890 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
891 MessageManager.getString("label.show_first"));
892 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
893 MessageManager.getString("label.show_last"));
894 buttonGroup.add(showAutoFirst);
895 buttonGroup.add(showAutoLast);
896 final boolean autoFirst = Cache.getDefault(
897 Preferences.SHOW_AUTOCALC_ABOVE, false);
898 showAutoFirst.setSelected(autoFirst);
899 setShowAutoCalculatedAbove(autoFirst);
900 showAutoFirst.addActionListener(new ActionListener()
903 public void actionPerformed(ActionEvent e)
905 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
906 sortAnnotations_actionPerformed();
909 showAutoLast.setSelected(!showAutoFirst.isSelected());
910 showAutoLast.addActionListener(new ActionListener()
913 public void actionPerformed(ActionEvent e)
915 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
916 sortAnnotations_actionPerformed();
920 JMenuItem deleteGroups = new JMenuItem(
921 MessageManager.getString("action.undefine_groups"));
922 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
923 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
924 al = new ActionListener()
927 public void actionPerformed(ActionEvent e)
929 deleteGroups_actionPerformed(e);
932 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
934 JMenuItem annotationColumn = new JMenuItem(
935 MessageManager.getString("action.select_by_annotation"));
936 annotationColumn.addActionListener(new ActionListener()
939 public void actionPerformed(ActionEvent e)
941 annotationColumn_actionPerformed(e);
945 JMenuItem createGroup = new JMenuItem(
946 MessageManager.getString("action.create_group"));
947 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
948 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
949 al = new ActionListener()
952 public void actionPerformed(ActionEvent e)
954 createGroup_actionPerformed(e);
957 addMenuActionAndAccelerator(keyStroke, createGroup, al);
959 JMenuItem unGroup = new JMenuItem(
960 MessageManager.getString("action.remove_group"));
961 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
962 .getDefaultToolkit().getMenuShortcutKeyMask()
963 | KeyEvent.SHIFT_MASK, false);
964 al = new ActionListener()
967 public void actionPerformed(ActionEvent e)
969 unGroup_actionPerformed(e);
972 addMenuActionAndAccelerator(keyStroke, unGroup, al);
974 copy.setText(MessageManager.getString("action.copy"));
975 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
976 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
978 al = new ActionListener()
981 public void actionPerformed(ActionEvent e)
983 copy_actionPerformed(e);
986 addMenuActionAndAccelerator(keyStroke, copy, al);
988 cut.setText(MessageManager.getString("action.cut"));
989 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
990 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
991 al = new ActionListener()
994 public void actionPerformed(ActionEvent e)
996 cut_actionPerformed(e);
999 addMenuActionAndAccelerator(keyStroke, cut, al);
1001 JMenuItem delete = new JMenuItem(
1002 MessageManager.getString("action.delete"));
1003 delete.addActionListener(new ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 delete_actionPerformed(e);
1012 pasteMenu.setText(MessageManager.getString("action.paste"));
1013 JMenuItem pasteNew = new JMenuItem(
1014 MessageManager.getString("label.to_new_alignment"));
1015 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1016 .getDefaultToolkit().getMenuShortcutKeyMask()
1017 | KeyEvent.SHIFT_MASK, false);
1018 al = new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 pasteNew_actionPerformed(e);
1026 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1028 JMenuItem pasteThis = new JMenuItem(
1029 MessageManager.getString("label.to_this_alignment"));
1030 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1031 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1032 al = new ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 pasteThis_actionPerformed(e);
1040 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1042 JMenuItem createPNG = new JMenuItem("PNG");
1043 createPNG.addActionListener(new ActionListener()
1046 public void actionPerformed(ActionEvent e)
1051 createPNG.setActionCommand(MessageManager
1052 .getString("label.save_png_image"));
1054 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1055 font.addActionListener(new ActionListener()
1058 public void actionPerformed(ActionEvent e)
1060 font_actionPerformed(e);
1063 seqLimits.setText(MessageManager
1064 .getString("label.show_sequence_limits"));
1065 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1066 seqLimits.addActionListener(new ActionListener()
1069 public void actionPerformed(ActionEvent e)
1071 seqLimit_actionPerformed(e);
1074 JMenuItem epsFile = new JMenuItem("EPS");
1075 epsFile.addActionListener(new ActionListener()
1078 public void actionPerformed(ActionEvent e)
1084 JMenuItem createSVG = new JMenuItem("SVG");
1085 createSVG.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1094 JMenuItem loadTreeMenuItem = new JMenuItem(
1095 MessageManager.getString("label.load_associated_tree"));
1096 loadTreeMenuItem.setActionCommand(MessageManager
1097 .getString("label.load_tree_for_sequence_set"));
1098 loadTreeMenuItem.addActionListener(new ActionListener()
1101 public void actionPerformed(ActionEvent e)
1103 loadTreeMenuItem_actionPerformed(e);
1107 scaleAbove.setVisible(false);
1108 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1109 scaleAbove.addActionListener(new ActionListener()
1112 public void actionPerformed(ActionEvent e)
1114 scaleAbove_actionPerformed(e);
1117 scaleLeft.setVisible(false);
1118 scaleLeft.setSelected(true);
1119 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1120 scaleLeft.addActionListener(new ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 scaleLeft_actionPerformed(e);
1128 scaleRight.setVisible(false);
1129 scaleRight.setSelected(true);
1130 scaleRight.setText(MessageManager.getString("action.scale_right"));
1131 scaleRight.addActionListener(new ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 scaleRight_actionPerformed(e);
1139 centreColumnLabelsMenuItem.setVisible(true);
1140 centreColumnLabelsMenuItem.setState(false);
1141 centreColumnLabelsMenuItem.setText(MessageManager
1142 .getString("label.centre_column_labels"));
1143 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 centreColumnLabels_actionPerformed(e);
1151 followHighlightMenuItem.setVisible(true);
1152 followHighlightMenuItem.setState(true);
1153 followHighlightMenuItem.setText(MessageManager
1154 .getString("label.automatic_scrolling"));
1155 followHighlightMenuItem.addActionListener(new ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 followHighlight_actionPerformed();
1167 .setText(MessageManager.getString("action.by_tree_order"));
1168 sort.setText(MessageManager.getString("action.sort"));
1169 sort.addMenuListener(new MenuListener()
1172 public void menuSelected(MenuEvent e)
1174 buildTreeSortMenu();
1178 public void menuDeselected(MenuEvent e)
1183 public void menuCanceled(MenuEvent e)
1187 sortByAnnotScore.setText(MessageManager
1188 .getString("label.sort_by_score"));
1189 sort.add(sortByAnnotScore);
1190 sort.addMenuListener(new javax.swing.event.MenuListener()
1194 public void menuCanceled(MenuEvent e)
1199 public void menuDeselected(MenuEvent e)
1204 public void menuSelected(MenuEvent e)
1206 buildSortByAnnotationScoresMenu();
1209 sortByAnnotScore.setVisible(false);
1211 calculateTree.setText(MessageManager
1212 .getString("action.calculate_tree_pca"));
1214 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1215 padGapsMenuitem.setState(jalview.bin.Cache
1216 .getDefault("PAD_GAPS", false));
1217 padGapsMenuitem.addActionListener(new ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 padGapsMenuitem_actionPerformed(e);
1225 JMenuItem vamsasStore = new JMenuItem(
1226 MessageManager.getString("label.vamsas_store"));
1227 vamsasStore.setVisible(false);
1228 vamsasStore.addActionListener(new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 vamsasStore_actionPerformed(e);
1236 showTranslation.setText(MessageManager
1237 .getString("label.translate_cDNA"));
1238 showTranslation.addActionListener(new ActionListener()
1241 public void actionPerformed(ActionEvent e)
1243 showTranslation_actionPerformed(e);
1246 showReverse.setText(MessageManager.getString("label.reverse"));
1247 showReverse.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 showReverse_actionPerformed(false);
1255 showReverseComplement.setText(MessageManager
1256 .getString("label.reverse_complement"));
1257 showReverseComplement.addActionListener(new ActionListener()
1260 public void actionPerformed(ActionEvent e)
1262 showReverse_actionPerformed(true);
1266 JMenuItem extractScores = new JMenuItem(
1267 MessageManager.getString("label.extract_scores"));
1268 extractScores.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 extractScores_actionPerformed(e);
1276 extractScores.setVisible(true);
1277 // JBPNote: TODO: make gui for regex based score extraction
1279 // for show products actions see AlignFrame.canShowProducts
1280 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1282 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1283 runGroovy.setToolTipText(MessageManager
1284 .getString("label.run_groovy_tip"));
1285 runGroovy.addActionListener(new ActionListener()
1288 public void actionPerformed(ActionEvent e)
1290 runGroovy_actionPerformed();
1294 JMenuItem openFeatureSettings = new JMenuItem(
1295 MessageManager.getString("action.feature_settings"));
1296 openFeatureSettings.addActionListener(new ActionListener()
1299 public void actionPerformed(ActionEvent e)
1301 featureSettings_actionPerformed(e);
1304 JMenuItem fetchSequence = new JMenuItem(
1305 MessageManager.getString("label.fetch_sequences"));
1306 fetchSequence.addActionListener(new ActionListener()
1309 public void actionPerformed(ActionEvent e)
1311 fetchSequence_actionPerformed(e);
1315 JMenuItem associatedData = new JMenuItem(
1316 MessageManager.getString("label.load_features_annotations"));
1317 associatedData.addActionListener(new ActionListener()
1320 public void actionPerformed(ActionEvent e)
1322 associatedData_actionPerformed(e);
1325 autoCalculate.setText(MessageManager
1326 .getString("label.autocalculate_consensus"));
1327 autoCalculate.setState(jalview.bin.Cache.getDefault(
1328 "AUTO_CALC_CONSENSUS", true));
1329 autoCalculate.addActionListener(new ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 autoCalculate_actionPerformed(e);
1337 sortByTree.setText(MessageManager
1338 .getString("label.sort_alignment_new_tree"));
1340 .setToolTipText("<html>"
1342 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1344 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1345 sortByTree.addActionListener(new ActionListener()
1348 public void actionPerformed(ActionEvent e)
1350 sortByTreeOption_actionPerformed(e);
1354 listenToViewSelections.setText(MessageManager
1355 .getString("label.listen_for_selections"));
1356 listenToViewSelections
1357 .setToolTipText("<html>"
1359 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1360 listenToViewSelections.setState(false);
1361 listenToViewSelections.addActionListener(new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 listenToViewSelections_actionPerformed(e);
1370 JMenu addSequenceMenu = new JMenu(
1371 MessageManager.getString("label.add_sequences"));
1372 JMenuItem addFromFile = new JMenuItem(
1373 MessageManager.getString("label.from_file"));
1374 addFromFile.addActionListener(new ActionListener()
1377 public void actionPerformed(ActionEvent e)
1379 addFromFile_actionPerformed(e);
1382 JMenuItem addFromText = new JMenuItem(
1383 MessageManager.getString("label.from_textbox"));
1384 addFromText.addActionListener(new ActionListener()
1387 public void actionPerformed(ActionEvent e)
1389 addFromText_actionPerformed(e);
1392 JMenuItem addFromURL = new JMenuItem(
1393 MessageManager.getString("label.from_url"));
1394 addFromURL.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 addFromURL_actionPerformed(e);
1402 JMenuItem exportFeatures = new JMenuItem(
1403 MessageManager.getString("label.export_features"));
1404 exportFeatures.addActionListener(new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 exportFeatures_actionPerformed(e);
1412 JMenuItem exportAnnotations = new JMenuItem(
1413 MessageManager.getString("label.export_annotations"));
1414 exportAnnotations.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent e)
1419 exportAnnotations_actionPerformed(e);
1422 statusPanel.setLayout(new GridLayout());
1423 JMenuItem showAllSeqs = new JMenuItem(
1424 MessageManager.getString("label.all_sequences"));
1425 showAllSeqs.setToolTipText(MessageManager
1426 .getString("label.toggle_sequence_visibility"));
1427 showAllSeqs.addActionListener(new ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 showAllSeqs_actionPerformed(e);
1435 JMenuItem showAllColumns = new JMenuItem(
1436 MessageManager.getString("label.all_columns"));
1437 showAllColumns.setToolTipText(MessageManager
1438 .getString("label.toggle_columns_visibility"));
1439 showAllColumns.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent e)
1444 showAllColumns_actionPerformed(e);
1447 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1448 JMenuItem hideSelSequences = new JMenuItem(
1449 MessageManager.getString("label.selected_sequences"));
1450 hideSelSequences.setToolTipText(MessageManager
1451 .getString("label.toggle_sequence_visibility"));
1452 hideSelSequences.addActionListener(new ActionListener()
1455 public void actionPerformed(ActionEvent e)
1457 hideSelSequences_actionPerformed(e);
1460 JMenuItem hideSelColumns = new JMenuItem(
1461 MessageManager.getString("label.selected_columns"));
1462 hideSelColumns.setToolTipText(MessageManager
1463 .getString("label.toggle_columns_visibility"));
1464 hideSelColumns.addActionListener(new ActionListener()
1467 public void actionPerformed(ActionEvent e)
1469 hideSelColumns_actionPerformed(e);
1472 JMenuItem hideAllSelection = new JMenuItem(
1473 MessageManager.getString("label.selected_region"));
1474 hideAllSelection.addActionListener(new ActionListener()
1477 public void actionPerformed(ActionEvent e)
1479 hideAllSelection_actionPerformed(e);
1482 // TODO: should be hidden if no selection exists.
1483 JMenuItem hideAllButSelection = new JMenuItem(
1484 MessageManager.getString("label.all_but_selected_region"));
1485 hideAllButSelection.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 hideAllButSelection_actionPerformed(e);
1493 JMenuItem showAllhidden = new JMenuItem(
1494 MessageManager.getString("label.all_sequences_columns"));
1495 showAllhidden.setToolTipText(MessageManager
1496 .getString("label.toggles_visibility_hidden_selected_regions"));
1497 showAllhidden.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent e)
1502 showAllhidden_actionPerformed(e);
1505 hiddenMarkers.setText(MessageManager
1506 .getString("action.show_hidden_markers"));
1507 hiddenMarkers.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 hiddenMarkers_actionPerformed(e);
1516 JMenuItem invertColSel = new JMenuItem(
1517 MessageManager.getString("action.invert_column_selection"));
1518 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1519 .getDefaultToolkit().getMenuShortcutKeyMask()
1520 | KeyEvent.ALT_MASK, false);
1521 al = new ActionListener()
1524 public void actionPerformed(ActionEvent e)
1526 invertColSel_actionPerformed(e);
1529 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1531 showComplementMenuItem.setVisible(false);
1532 showComplementMenuItem.addActionListener(new ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 showComplement_actionPerformed(showComplementMenuItem.getState());
1541 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1544 public void stateChanged(ChangeEvent evt)
1546 JTabbedPane pane = (JTabbedPane) evt.getSource();
1547 int sel = pane.getSelectedIndex();
1548 tabSelectionChanged(sel);
1551 tabbedPane.addMouseListener(new MouseAdapter()
1554 public void mousePressed(MouseEvent e)
1556 if (e.isPopupTrigger()) // Mac
1558 tabbedPane_mousePressed(e);
1563 public void mouseReleased(MouseEvent e)
1565 if (e.isPopupTrigger()) // Windows
1567 tabbedPane_mousePressed(e);
1571 tabbedPane.addFocusListener(new FocusAdapter()
1574 public void focusGained(FocusEvent e)
1576 tabbedPane_focusGained(e);
1580 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1581 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1582 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1583 al = new ActionListener()
1586 public void actionPerformed(ActionEvent e)
1588 save_actionPerformed(e);
1591 addMenuActionAndAccelerator(keyStroke, save, al);
1593 reload.setEnabled(false);
1594 reload.setText(MessageManager.getString("action.reload"));
1595 reload.addActionListener(new ActionListener()
1598 public void actionPerformed(ActionEvent e)
1600 reload_actionPerformed(e);
1604 JMenuItem newView = new JMenuItem(
1605 MessageManager.getString("action.new_view"));
1606 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1607 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1608 al = new ActionListener()
1611 public void actionPerformed(ActionEvent e)
1613 newView_actionPerformed(e);
1616 addMenuActionAndAccelerator(keyStroke, newView, al);
1618 tabbedPane.setToolTipText("<html><i>"
1619 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1622 formatMenu.setText(MessageManager.getString("action.format"));
1623 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1625 idRightAlign.setText(MessageManager
1626 .getString("label.right_align_sequence_id"));
1627 idRightAlign.addActionListener(new ActionListener()
1630 public void actionPerformed(ActionEvent e)
1632 idRightAlign_actionPerformed(e);
1636 gatherViews.setEnabled(false);
1637 gatherViews.setText(MessageManager.getString("action.gather_views"));
1638 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1639 al = new ActionListener()
1642 public void actionPerformed(ActionEvent e)
1644 gatherViews_actionPerformed(e);
1647 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1649 expandViews.setEnabled(false);
1650 expandViews.setText(MessageManager.getString("action.expand_views"));
1651 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1652 al = new ActionListener()
1655 public void actionPerformed(ActionEvent e)
1657 expandViews_actionPerformed(e);
1660 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1662 JMenuItem pageSetup = new JMenuItem(
1663 MessageManager.getString("action.page_setup"));
1664 pageSetup.addActionListener(new ActionListener()
1667 public void actionPerformed(ActionEvent e)
1669 pageSetup_actionPerformed(e);
1672 JMenuItem alignmentProperties = new JMenuItem(
1673 MessageManager.getString("label.alignment_props"));
1674 alignmentProperties.addActionListener(new ActionListener()
1677 public void actionPerformed(ActionEvent actionEvent)
1679 alignmentProperties();
1682 JMenuItem selectHighlighted = new JMenuItem(
1683 MessageManager.getString("action.select_highlighted_columns"));
1684 selectHighlighted.setToolTipText(MessageManager
1685 .getString("tooltip.select_highlighted_columns"));
1686 al = new ActionListener()
1689 public void actionPerformed(ActionEvent actionEvent)
1691 selectHighlightedColumns_actionPerformed(actionEvent);
1694 hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
1695 hmmBuild.addActionListener(new ActionListener()
1699 public void actionPerformed(ActionEvent e)
1703 hmmBuild_actionPerformed(e);
1704 } catch (IOException e1)
1706 // TODO Auto-generated catch block
1707 e1.printStackTrace();
1708 } catch (InterruptedException e1)
1710 // TODO Auto-generated catch block
1711 e1.printStackTrace();
1716 selectHighlighted.addActionListener(al);
1717 JMenu tooltipSettingsMenu = new JMenu(
1718 MessageManager.getString("label.sequence_id_tooltip"));
1719 JMenu autoAnnMenu = new JMenu(
1720 MessageManager.getString("label.autocalculated_annotation"));
1722 JMenu exportImageMenu = new JMenu(
1723 MessageManager.getString("label.export_image"));
1724 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1725 alignFrameMenuBar.add(fileMenu);
1726 alignFrameMenuBar.add(editMenu);
1727 alignFrameMenuBar.add(selectMenu);
1728 alignFrameMenuBar.add(viewMenu);
1729 alignFrameMenuBar.add(annotationsMenu);
1730 alignFrameMenuBar.add(formatMenu);
1731 alignFrameMenuBar.add(colourMenu);
1732 alignFrameMenuBar.add(calculateMenu);
1733 alignFrameMenuBar.add(webService);
1734 alignFrameMenuBar.add(hmmerMenu);
1736 fileMenu.add(fetchSequence);
1737 fileMenu.add(addSequenceMenu);
1738 fileMenu.add(reload);
1739 fileMenu.addSeparator();
1740 fileMenu.add(vamsasStore);
1742 fileMenu.add(saveAs);
1743 fileMenu.add(outputTextboxMenu);
1744 fileMenu.add(pageSetup);
1745 fileMenu.add(printMenuItem);
1746 fileMenu.addSeparator();
1747 fileMenu.add(exportImageMenu);
1748 fileMenu.add(exportFeatures);
1749 fileMenu.add(exportAnnotations);
1750 fileMenu.add(loadTreeMenuItem);
1751 fileMenu.add(associatedData);
1752 fileMenu.addSeparator();
1753 fileMenu.add(closeMenuItem);
1755 pasteMenu.add(pasteNew);
1756 pasteMenu.add(pasteThis);
1757 editMenu.add(undoMenuItem);
1758 editMenu.add(redoMenuItem);
1761 editMenu.add(pasteMenu);
1762 editMenu.add(delete);
1763 editMenu.addSeparator();
1764 editMenu.add(remove2LeftMenuItem);
1765 editMenu.add(remove2RightMenuItem);
1766 editMenu.add(removeGappedColumnMenuItem);
1767 editMenu.add(removeAllGapsMenuItem);
1768 editMenu.add(removeRedundancyMenuItem);
1769 editMenu.addSeparator();
1770 // dont add these yet in the CVS build - they cannot be undone!
1771 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1772 // editMenu.add(justifyLeftMenuItem);
1773 // editMenu.add(justifyRightMenuItem);
1774 // editMenu.addSeparator();
1775 editMenu.add(padGapsMenuitem);
1777 showMenu.add(showAllColumns);
1778 showMenu.add(showAllSeqs);
1779 showMenu.add(showAllhidden);
1780 hideMenu.add(hideSelColumns);
1781 hideMenu.add(hideSelSequences);
1782 hideMenu.add(hideAllSelection);
1783 hideMenu.add(hideAllButSelection);
1784 viewMenu.add(newView);
1785 viewMenu.add(expandViews);
1786 viewMenu.add(gatherViews);
1787 viewMenu.addSeparator();
1788 viewMenu.add(showMenu);
1789 viewMenu.add(hideMenu);
1790 viewMenu.add(showComplementMenuItem);
1791 viewMenu.addSeparator();
1792 viewMenu.add(followHighlightMenuItem);
1793 viewMenu.addSeparator();
1794 viewMenu.add(showSeqFeatures);
1795 // viewMenu.add(showSeqFeaturesHeight);
1796 viewMenu.add(openFeatureSettings);
1797 tooltipSettingsMenu.add(showDbRefsMenuitem);
1798 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1799 viewMenu.add(tooltipSettingsMenu);
1800 viewMenu.addSeparator();
1801 viewMenu.add(alignmentProperties);
1802 viewMenu.addSeparator();
1803 viewMenu.add(overviewMenuItem);
1805 annotationsMenu.add(annotationPanelMenuItem);
1806 annotationsMenu.addSeparator();
1807 annotationsMenu.add(showAllAlAnnotations);
1808 annotationsMenu.add(hideAllAlAnnotations);
1809 annotationsMenu.addSeparator();
1810 annotationsMenu.add(showAllSeqAnnotations);
1811 annotationsMenu.add(hideAllSeqAnnotations);
1812 annotationsMenu.add(sortAnnBySequence);
1813 annotationsMenu.add(sortAnnByLabel);
1814 annotationsMenu.addSeparator();
1815 autoAnnMenu.add(showAutoFirst);
1816 autoAnnMenu.add(showAutoLast);
1817 autoAnnMenu.addSeparator();
1818 autoAnnMenu.add(applyAutoAnnotationSettings);
1819 autoAnnMenu.add(showConsensusHistogram);
1820 autoAnnMenu.add(showSequenceLogo);
1821 autoAnnMenu.add(normaliseSequenceLogo);
1822 autoAnnMenu.addSeparator();
1823 autoAnnMenu.add(showGroupConservation);
1824 autoAnnMenu.add(showGroupConsensus);
1825 annotationsMenu.add(autoAnnMenu);
1828 sort.add(sortIDMenuItem);
1829 sort.add(sortLengthMenuItem);
1830 sort.add(sortGroupMenuItem);
1831 sort.add(sortPairwiseMenuItem);
1832 sort.add(sortByTreeMenu);
1833 calculateMenu.add(sort);
1834 calculateMenu.add(calculateTree);
1835 calculateMenu.addSeparator();
1836 calculateMenu.add(pairwiseAlignmentMenuItem);
1837 calculateMenu.addSeparator();
1838 calculateMenu.add(showTranslation);
1839 calculateMenu.add(showReverse);
1840 calculateMenu.add(showReverseComplement);
1841 calculateMenu.add(showProducts);
1842 calculateMenu.add(autoCalculate);
1843 calculateMenu.add(sortByTree);
1844 calculateMenu.addSeparator();
1845 calculateMenu.add(expandAlignment);
1846 calculateMenu.add(extractScores);
1847 calculateMenu.addSeparator();
1848 calculateMenu.add(runGroovy);
1850 webServiceNoServices = new JMenuItem(
1851 MessageManager.getString("label.no_services"));
1852 webService.add(webServiceNoServices);
1853 exportImageMenu.add(htmlMenuItem);
1854 exportImageMenu.add(epsFile);
1855 exportImageMenu.add(createPNG);
1856 exportImageMenu.add(createBioJS);
1857 exportImageMenu.add(createSVG);
1858 addSequenceMenu.add(addFromFile);
1859 addSequenceMenu.add(addFromText);
1860 addSequenceMenu.add(addFromURL);
1861 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1862 statusPanel.add(statusBar, null);
1863 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1865 formatMenu.add(font);
1866 formatMenu.addSeparator();
1867 formatMenu.add(wrapMenuItem);
1868 formatMenu.add(scaleAbove);
1869 formatMenu.add(scaleLeft);
1870 formatMenu.add(scaleRight);
1871 formatMenu.add(seqLimits);
1872 formatMenu.add(idRightAlign);
1873 formatMenu.add(hiddenMarkers);
1874 formatMenu.add(viewBoxesMenuItem);
1875 formatMenu.add(viewTextMenuItem);
1876 formatMenu.add(colourTextMenuItem);
1877 formatMenu.add(renderGapsMenuItem);
1878 formatMenu.add(centreColumnLabelsMenuItem);
1879 formatMenu.add(showNonconservedMenuItem);
1880 selectMenu.add(findMenuItem);
1881 selectMenu.addSeparator();
1882 selectMenu.add(selectAllSequenceMenuItem);
1883 selectMenu.add(deselectAllSequenceMenuItem);
1884 selectMenu.add(invertSequenceMenuItem);
1885 selectMenu.add(invertColSel);
1886 selectMenu.add(createGroup);
1887 selectMenu.add(unGroup);
1888 selectMenu.add(grpsFromSelection);
1889 selectMenu.add(deleteGroups);
1890 selectMenu.add(annotationColumn);
1891 selectMenu.add(selectHighlighted);
1892 // TODO - determine if the listenToViewSelections button is needed : see bug
1894 // selectMenu.addSeparator();
1895 // selectMenu.add(listenToViewSelections);
1899 * Constructs the entries on the Colour menu (but does not add them to the
1902 protected void initHMMERMenu()
1904 autoAlignSeqs = new JCheckBoxMenuItem(
1905 MessageManager.getString("label.auto_align_seqs"));
1906 hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
1907 hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
1908 hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
1909 autoAlignSeqs.addActionListener(new ActionListener()
1912 public void actionPerformed(ActionEvent e)
1914 autoAlignSeqs_actionPerformed(autoAlignSeqs.isSelected());
1919 protected void initColourMenu()
1921 applyToAllGroups = new JCheckBoxMenuItem(
1922 MessageManager.getString("label.apply_colour_to_all_groups"));
1923 applyToAllGroups.addActionListener(new ActionListener()
1926 public void actionPerformed(ActionEvent e)
1928 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1932 textColour = new JMenuItem(
1933 MessageManager.getString("label.text_colour"));
1934 textColour.addActionListener(new ActionListener()
1937 public void actionPerformed(ActionEvent e)
1939 textColour_actionPerformed();
1943 conservationMenuItem = new JCheckBoxMenuItem(
1944 MessageManager.getString("action.by_conservation"));
1945 conservationMenuItem.addActionListener(new ActionListener()
1948 public void actionPerformed(ActionEvent e)
1950 conservationMenuItem_actionPerformed(conservationMenuItem
1955 abovePIDThreshold = new JCheckBoxMenuItem(
1956 MessageManager.getString("label.above_identity_threshold"));
1957 abovePIDThreshold.addActionListener(new ActionListener()
1960 public void actionPerformed(ActionEvent e)
1962 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1965 modifyPID = new JMenuItem(
1966 MessageManager.getString("label.modify_identity_threshold"));
1967 modifyPID.addActionListener(new ActionListener()
1970 public void actionPerformed(ActionEvent e)
1972 modifyPID_actionPerformed();
1975 modifyConservation = new JMenuItem(
1977 .getString("label.modify_conservation_threshold"));
1978 modifyConservation.addActionListener(new ActionListener()
1981 public void actionPerformed(ActionEvent e)
1983 modifyConservation_actionPerformed();
1987 annotationColour = new JMenuItem(
1988 MessageManager.getString("action.by_annotation"));
1989 annotationColour.addActionListener(new ActionListener()
1992 public void actionPerformed(ActionEvent e)
1994 annotationColour_actionPerformed();
1999 protected void selectHighlightedColumns_actionPerformed(
2000 ActionEvent actionEvent)
2002 // TODO Auto-generated method stub
2007 * Generate the reverse sequence (or reverse complement if the flag is true)
2008 * and add it to the alignment
2012 protected void showReverse_actionPerformed(boolean complement)
2017 * Try to run script in a Groovy console, having first ensured that this
2018 * alignframe is set as currentAlignFrame in Desktop
2020 protected void runGroovy_actionPerformed()
2026 * Adds the given action listener and key accelerator to the given menu item.
2027 * Also saves in a lookup table to support lookup of action by key stroke.
2031 * @param actionListener
2033 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2034 JMenuItem menuItem, ActionListener actionListener)
2036 menuItem.setAccelerator(keyStroke);
2037 accelerators.put(keyStroke, menuItem);
2038 menuItem.addActionListener(actionListener);
2042 * Action on clicking sort annotations by type.
2046 protected void sortAnnotations_actionPerformed()
2051 * Action on clicking Show all annotations.
2053 * @param forSequences
2054 * update sequence-related annotations
2055 * @param forAlignment
2056 * update non-sequence-related annotations
2058 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2059 boolean forAlignment)
2061 setAnnotationsVisibility(true, forSequences, forAlignment);
2065 * Action on clicking Hide all annotations.
2067 * @param forSequences
2068 * update sequence-related annotations
2069 * @param forAlignment
2070 * update non-sequence-related annotations
2072 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2073 boolean forAlignment)
2075 setAnnotationsVisibility(false, forSequences, forAlignment);
2079 * Set the visibility of annotations to true or false. Can act on
2080 * sequence-related annotations, or alignment-related, or both.
2083 * @param forSequences
2084 * update sequence-related annotations
2085 * @param forAlignment
2086 * update non-sequence-related annotations
2088 protected void setAnnotationsVisibility(boolean visible,
2089 boolean forSequences, boolean forAlignment)
2094 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2096 // TODO Auto-generated method stub
2100 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2102 // TODO Auto-generated method stub
2106 protected void showAllhidden_actionPerformed(ActionEvent e)
2108 // TODO Auto-generated method stub
2112 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2114 // TODO Auto-generated method stub
2118 protected void hideAllSelection_actionPerformed(ActionEvent e)
2120 // TODO Auto-generated method stub
2124 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2126 // TODO Auto-generated method stub
2130 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2132 // TODO Auto-generated method stub
2136 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2138 // TODO Auto-generated method stub
2142 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2144 // TODO Auto-generated method stub
2148 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2150 // TODO Auto-generated method stub
2154 protected void showGroupConservation_actionPerformed(ActionEvent e)
2156 // TODO Auto-generated method stub
2160 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2162 // TODO Auto-generated method stub
2166 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2168 // TODO Auto-generated method stub
2172 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2174 // TODO Auto-generated method stub
2178 protected void followHighlight_actionPerformed()
2180 // TODO Auto-generated method stub
2184 protected void showNpFeats_actionPerformed(ActionEvent e)
2186 // TODO Auto-generated method stub
2190 protected void showDbRefs_actionPerformed(ActionEvent e)
2192 // TODO Auto-generated method stub
2196 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2200 protected void buildSortByAnnotationScoresMenu()
2204 protected void extractScores_actionPerformed(ActionEvent e)
2208 protected void outputText_actionPerformed(ActionEvent e)
2212 public void addFromFile_actionPerformed(ActionEvent e)
2217 public void addFromText_actionPerformed(ActionEvent e)
2222 public void addFromURL_actionPerformed(ActionEvent e)
2227 public void exportFeatures_actionPerformed(ActionEvent e)
2232 public void exportAnnotations_actionPerformed(ActionEvent e)
2237 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2241 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2246 protected void closeMenuItem_actionPerformed(boolean b)
2250 protected void redoMenuItem_actionPerformed(ActionEvent e)
2254 protected void undoMenuItem_actionPerformed(ActionEvent e)
2258 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2262 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2266 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2270 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2274 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2278 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2282 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2286 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2290 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2294 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2298 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2302 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2306 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2310 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2314 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2318 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2322 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2326 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2330 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2334 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2338 protected void conservationMenuItem_actionPerformed(boolean selected)
2342 protected void printMenuItem_actionPerformed(ActionEvent e)
2346 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2350 protected void findMenuItem_actionPerformed(ActionEvent e)
2354 protected void abovePIDThreshold_actionPerformed(boolean selected)
2358 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2362 protected void deleteGroups_actionPerformed(ActionEvent e)
2366 protected void createGroup_actionPerformed(ActionEvent e)
2370 protected void unGroup_actionPerformed(ActionEvent e)
2374 protected void copy_actionPerformed(ActionEvent e)
2378 protected void cut_actionPerformed(ActionEvent e)
2382 protected void delete_actionPerformed(ActionEvent e)
2386 protected void pasteNew_actionPerformed(ActionEvent e)
2390 protected void pasteThis_actionPerformed(ActionEvent e)
2394 protected void applyToAllGroups_actionPerformed(boolean selected)
2398 protected void autoAlignSeqs_actionPerformed(boolean selected)
2402 protected void hmmAlign_actionPerformed(ActionEvent e)
2406 protected void hmmBuild_actionPerformed(ActionEvent e)
2407 throws IOException, InterruptedException
2411 protected void hmmSearch_actionPerformed(ActionEvent e)
2415 public void createPNG(java.io.File f)
2419 protected void font_actionPerformed(ActionEvent e)
2423 protected void seqLimit_actionPerformed(ActionEvent e)
2427 public void seqDBRef_actionPerformed(ActionEvent e)
2432 public void createEPS(java.io.File f)
2436 public void createSVG(java.io.File f)
2441 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2447 * Template method to handle the 'load T-Coffee scores' menu event.
2449 * Subclasses override this method to provide a custom action.
2454 protected void loadScores_actionPerformed(ActionEvent event)
2459 protected void jpred_actionPerformed(ActionEvent e)
2463 protected void scaleAbove_actionPerformed(ActionEvent e)
2467 protected void scaleLeft_actionPerformed(ActionEvent e)
2471 protected void scaleRight_actionPerformed(ActionEvent e)
2475 protected void modifyPID_actionPerformed()
2479 protected void modifyConservation_actionPerformed()
2483 protected void saveAs_actionPerformed(ActionEvent e)
2487 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2491 public void vamsasStore_actionPerformed(ActionEvent e)
2496 public void vamsasLoad_actionPerformed(ActionEvent e)
2501 public void showTranslation_actionPerformed(ActionEvent e)
2506 public void featureSettings_actionPerformed(ActionEvent e)
2511 public void fetchSequence_actionPerformed(ActionEvent e)
2516 public void smoothFont_actionPerformed(ActionEvent e)
2521 public void annotationColour_actionPerformed()
2525 public void annotationColumn_actionPerformed(ActionEvent e)
2529 public void associatedData_actionPerformed(ActionEvent e)
2534 public void autoCalculate_actionPerformed(ActionEvent e)
2539 public void sortByTreeOption_actionPerformed(ActionEvent e)
2544 public void showAllSeqs_actionPerformed(ActionEvent e)
2549 public void showAllColumns_actionPerformed(ActionEvent e)
2554 public void hideSelSequences_actionPerformed(ActionEvent e)
2559 public void hideSelColumns_actionPerformed(ActionEvent e)
2564 public void hiddenMarkers_actionPerformed(ActionEvent e)
2569 public void findPdbId_actionPerformed(ActionEvent e)
2574 public void enterPdbId_actionPerformed(ActionEvent e)
2579 public void pdbFile_actionPerformed(ActionEvent e)
2584 public void invertColSel_actionPerformed(ActionEvent e)
2589 public void tabSelectionChanged(int sel)
2594 public void tabbedPane_mousePressed(MouseEvent e)
2599 public void tabbedPane_focusGained(FocusEvent e)
2604 public void save_actionPerformed(ActionEvent e)
2609 public void reload_actionPerformed(ActionEvent e)
2614 public void newView_actionPerformed(ActionEvent e)
2619 public void textColour_actionPerformed()
2624 public void idRightAlign_actionPerformed(ActionEvent e)
2629 public void expandViews_actionPerformed(ActionEvent e)
2634 public void gatherViews_actionPerformed(ActionEvent e)
2639 public void buildTreeSortMenu()
2644 public void pageSetup_actionPerformed(ActionEvent e)
2649 public void alignmentProperties()
2654 protected void expand_newalign(ActionEvent e)
2656 // TODO Auto-generated method stub
2660 protected boolean isShowAutoCalculatedAbove()
2662 return showAutoCalculatedAbove;
2665 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2667 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2670 protected SequenceAnnotationOrder getAnnotationSortOrder()
2672 return annotationSortOrder;
2675 protected void setAnnotationSortOrder(
2676 SequenceAnnotationOrder annotationSortOrder)
2678 this.annotationSortOrder = annotationSortOrder;
2681 public Map<KeyStroke, JMenuItem> getAccelerators()
2683 return this.accelerators;
2687 * Returns the selected index of the tabbed pane, or -1 if none selected
2688 * (including the case where the tabbed pane has not been made visible).
2692 public int getTabIndex()
2694 return tabbedPane.getSelectedIndex();
2697 public JPanel getStatusPanel()
2703 * Sets a reference to the containing split frame. Also makes the 'toggle
2704 * split view' menu item visible and checked.
2708 public void setSplitFrame(SplitContainerI sf)
2710 this.splitFrame = sf;
2713 this.showComplementMenuItem.setVisible(true);
2714 this.showComplementMenuItem.setState(true);
2718 public SplitContainerI getSplitViewContainer()
2720 return this.splitFrame;
2723 protected void showComplement_actionPerformed(boolean complement)
2727 protected void showInformationHistogram_actionPerformed(ActionEvent e)
2729 // TODO Auto-generated method stub
2733 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2735 // TODO Auto-generated method stub
2739 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2741 // TODO Auto-generated method stub