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 JMenuItem hmmAlign = new JMenuItem();
75 protected JMenuItem hmmSearch = new JMenuItem();
77 protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
79 protected JMenuItem webServiceNoServices;
81 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
83 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
85 protected JMenu sortByAnnotScore = new JMenu();
87 public JLabel statusBar = new JLabel();
89 protected JMenu outputTextboxMenu = new JMenu();
91 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
93 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
95 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
97 protected JMenuItem undoMenuItem = new JMenuItem();
99 protected JMenuItem redoMenuItem = new JMenuItem();
101 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
103 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
105 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
107 JMenuItem copy = new JMenuItem();
109 JMenuItem cut = new JMenuItem();
111 JMenu pasteMenu = new JMenu();
113 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
115 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
117 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
119 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
121 protected JCheckBoxMenuItem applyToAllGroups;
123 protected JMenu colourMenu = new JMenu();
125 protected JMenuItem textColour;
127 protected JCheckBoxMenuItem conservationMenuItem;
129 protected JMenuItem modifyConservation;
131 protected JCheckBoxMenuItem abovePIDThreshold;
133 protected JMenuItem modifyPID;
135 protected JMenuItem annotationColour;
137 protected JMenu sortByTreeMenu = new JMenu();
139 protected JMenu sort = new JMenu();
141 protected JMenuItem calculateTree = new JMenuItem();
143 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
145 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
147 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
149 protected JMenuItem showTranslation = new JMenuItem();
151 protected JMenuItem showReverse = new JMenuItem();
153 protected JMenuItem showReverseComplement = new JMenuItem();
155 protected JMenu showProducts = new JMenu();
157 protected JMenuItem runGroovy = new JMenuItem();
159 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
161 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
163 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
165 protected JPanel statusPanel = new JPanel();
167 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
169 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
171 protected JMenuItem showAllAlAnnotations = new JMenuItem();
173 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
175 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
177 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
179 protected JTabbedPane tabbedPane = new JTabbedPane();
181 protected JMenuItem reload = new JMenuItem();
183 protected JMenu formatMenu = new JMenu();
185 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
187 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
189 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
191 protected JMenuItem gatherViews = new JMenuItem();
193 protected JMenuItem expandViews = new JMenuItem();
195 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
203 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
209 protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
211 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
213 private SequenceAnnotationOrder annotationSortOrder;
215 private boolean showAutoCalculatedAbove = false;
217 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
219 private SplitContainerI splitFrame;
226 setJMenuBar(alignFrameMenuBar);
228 // dynamically fill save as menu with available formats
229 for (String ff : FileFormats.getInstance().getWritableFormats(true))
231 JMenuItem item = new JMenuItem(ff);
233 item.addActionListener(new ActionListener()
236 public void actionPerformed(ActionEvent e)
238 outputText_actionPerformed(e);
242 outputTextboxMenu.add(item);
244 } catch (Exception e)
246 System.err.println(e.toString());
249 if (!Platform.isAMac())
251 closeMenuItem.setMnemonic('C');
252 outputTextboxMenu.setMnemonic('T');
253 undoMenuItem.setMnemonic('Z');
254 redoMenuItem.setMnemonic('0');
255 copy.setMnemonic('C');
256 cut.setMnemonic('U');
257 pasteMenu.setMnemonic('P');
258 reload.setMnemonic('R');
262 private void jbInit() throws Exception
267 JMenuItem saveAs = new JMenuItem(
268 MessageManager.getString("action.save_as"));
269 ActionListener al = new ActionListener()
272 public void actionPerformed(ActionEvent e)
274 saveAs_actionPerformed(e);
278 // FIXME getDefaultToolkit throws an exception in Headless mode
279 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
280 .getDefaultToolkit().getMenuShortcutKeyMask()
281 | KeyEvent.SHIFT_MASK, false);
282 addMenuActionAndAccelerator(keyStroke, saveAs, al);
284 closeMenuItem.setText(MessageManager.getString("action.close"));
285 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
286 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
287 al = new ActionListener()
290 public void actionPerformed(ActionEvent e)
292 closeMenuItem_actionPerformed(false);
295 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
297 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
298 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
299 JMenu annotationsMenu = new JMenu(
300 MessageManager.getString("action.annotations"));
301 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
302 colourMenu.setText(MessageManager.getString("action.colour"));
303 JMenu calculateMenu = new JMenu(
304 MessageManager.getString("action.calculate"));
305 webService.setText(MessageManager.getString("action.web_service"));
306 hmmerMenu.setText(MessageManager.getString("action.hmmer"));
307 String status = Cache.getProperty("HMMER_FUNCTIONING");
308 if ("false".equals(status) || status == null)
310 hmmerMenu.setEnabled(false);
314 hmmerMenu.setEnabled(true);
316 hmmerMenu.addActionListener(new ActionListener()
319 public void actionPerformed(ActionEvent e)
321 hmmerMenu_actionPerformed(e);
324 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
325 MessageManager.getString("action.select_all"));
326 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
327 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
328 al = new ActionListener()
331 public void actionPerformed(ActionEvent e)
333 selectAllSequenceMenuItem_actionPerformed(e);
336 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
338 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
339 MessageManager.getString("action.deselect_all"));
340 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
341 al = new ActionListener()
344 public void actionPerformed(ActionEvent e)
346 deselectAllSequenceMenuItem_actionPerformed(e);
349 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
351 JMenuItem invertSequenceMenuItem = new JMenuItem(
352 MessageManager.getString("action.invert_sequence_selection"));
353 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
354 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
355 al = new ActionListener()
358 public void actionPerformed(ActionEvent e)
360 invertSequenceMenuItem_actionPerformed(e);
363 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
365 JMenuItem grpsFromSelection = new JMenuItem(
366 MessageManager.getString("action.make_groups_selection"));
367 grpsFromSelection.addActionListener(new ActionListener()
370 public void actionPerformed(ActionEvent e)
372 makeGrpsFromSelection_actionPerformed(e);
375 JMenuItem expandAlignment = new JMenuItem(
376 MessageManager.getString("action.view_flanking_regions"));
377 expandAlignment.setToolTipText(MessageManager
378 .getString("label.view_flanking_regions"));
379 expandAlignment.addActionListener(new ActionListener()
382 public void actionPerformed(ActionEvent e)
387 JMenuItem remove2LeftMenuItem = new JMenuItem(
388 MessageManager.getString("action.remove_left"));
389 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
390 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
391 al = new ActionListener()
394 public void actionPerformed(ActionEvent e)
396 remove2LeftMenuItem_actionPerformed(e);
399 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
401 JMenuItem remove2RightMenuItem = new JMenuItem(
402 MessageManager.getString("action.remove_right"));
403 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
404 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
405 al = new ActionListener()
408 public void actionPerformed(ActionEvent e)
410 remove2RightMenuItem_actionPerformed(e);
413 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
415 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
416 MessageManager.getString("action.remove_empty_columns"));
417 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
418 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
419 al = new ActionListener()
422 public void actionPerformed(ActionEvent e)
424 removeGappedColumnMenuItem_actionPerformed(e);
427 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
429 JMenuItem removeAllGapsMenuItem = new JMenuItem(
430 MessageManager.getString("action.remove_all_gaps"));
431 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
432 .getDefaultToolkit().getMenuShortcutKeyMask()
433 | KeyEvent.SHIFT_MASK, false);
434 al = new ActionListener()
437 public void actionPerformed(ActionEvent e)
439 removeAllGapsMenuItem_actionPerformed(e);
442 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
444 JMenuItem justifyLeftMenuItem = new JMenuItem(
445 MessageManager.getString("action.left_justify_alignment"));
446 justifyLeftMenuItem.addActionListener(new ActionListener()
449 public void actionPerformed(ActionEvent e)
451 justifyLeftMenuItem_actionPerformed(e);
454 JMenuItem justifyRightMenuItem = new JMenuItem(
455 MessageManager.getString("action.right_justify_alignment"));
456 justifyRightMenuItem.addActionListener(new ActionListener()
459 public void actionPerformed(ActionEvent e)
461 justifyRightMenuItem_actionPerformed(e);
464 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
465 viewBoxesMenuItem.setState(true);
466 viewBoxesMenuItem.addActionListener(new ActionListener()
469 public void actionPerformed(ActionEvent e)
471 viewBoxesMenuItem_actionPerformed(e);
474 viewTextMenuItem.setText(MessageManager.getString("action.text"));
475 viewTextMenuItem.setState(true);
476 viewTextMenuItem.addActionListener(new ActionListener()
479 public void actionPerformed(ActionEvent e)
481 viewTextMenuItem_actionPerformed(e);
484 showNonconservedMenuItem.setText(MessageManager
485 .getString("label.show_non_conserved"));
486 showNonconservedMenuItem.setState(false);
487 showNonconservedMenuItem.addActionListener(new ActionListener()
490 public void actionPerformed(ActionEvent e)
492 showUnconservedMenuItem_actionPerformed(e);
495 JMenuItem sortPairwiseMenuItem = new JMenuItem(
496 MessageManager.getString("action.by_pairwise_id"));
497 sortPairwiseMenuItem.addActionListener(new ActionListener()
500 public void actionPerformed(ActionEvent e)
502 sortPairwiseMenuItem_actionPerformed(e);
505 JMenuItem sortIDMenuItem = new JMenuItem(
506 MessageManager.getString("action.by_id"));
507 sortIDMenuItem.addActionListener(new ActionListener()
510 public void actionPerformed(ActionEvent e)
512 sortIDMenuItem_actionPerformed(e);
515 JMenuItem sortLengthMenuItem = new JMenuItem(
516 MessageManager.getString("action.by_length"));
517 sortLengthMenuItem.addActionListener(new ActionListener()
520 public void actionPerformed(ActionEvent e)
522 sortLengthMenuItem_actionPerformed(e);
525 JMenuItem sortGroupMenuItem = new JMenuItem(
526 MessageManager.getString("action.by_group"));
527 sortGroupMenuItem.addActionListener(new ActionListener()
530 public void actionPerformed(ActionEvent e)
532 sortGroupMenuItem_actionPerformed(e);
536 JMenuItem removeRedundancyMenuItem = new JMenuItem(
537 MessageManager.getString("action.remove_redundancy"));
538 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
539 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
540 al = new ActionListener()
543 public void actionPerformed(ActionEvent e)
545 removeRedundancyMenuItem_actionPerformed(e);
548 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
550 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
551 MessageManager.getString("action.pairwise_alignment"));
552 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
555 public void actionPerformed(ActionEvent e)
557 pairwiseAlignmentMenuItem_actionPerformed(e);
561 this.getContentPane().setLayout(new BorderLayout());
562 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
563 statusBar.setBackground(Color.white);
564 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
565 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
566 statusBar.setText(MessageManager.getString("label.status_bar"));
567 outputTextboxMenu.setText(MessageManager
568 .getString("label.out_to_textbox"));
570 annotationPanelMenuItem.setActionCommand("");
571 annotationPanelMenuItem.setText(MessageManager
572 .getString("label.show_annotations"));
573 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
575 annotationPanelMenuItem.addActionListener(new ActionListener()
578 public void actionPerformed(ActionEvent e)
580 annotationPanelMenuItem_actionPerformed(e);
583 showAllAlAnnotations.setText(MessageManager
584 .getString("label.show_all_al_annotations"));
585 final boolean isAnnotationPanelShown = annotationPanelMenuItem
587 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
588 showAllAlAnnotations.addActionListener(new ActionListener()
591 public void actionPerformed(ActionEvent e)
593 showAllAnnotations_actionPerformed(false, true);
596 hideAllAlAnnotations.setText(MessageManager
597 .getString("label.hide_all_al_annotations"));
598 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
599 hideAllAlAnnotations.addActionListener(new ActionListener()
602 public void actionPerformed(ActionEvent e)
604 hideAllAnnotations_actionPerformed(false, true);
607 showAllSeqAnnotations.setText(MessageManager
608 .getString("label.show_all_seq_annotations"));
609 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
610 showAllSeqAnnotations.addActionListener(new ActionListener()
613 public void actionPerformed(ActionEvent e)
615 showAllAnnotations_actionPerformed(true, false);
618 hideAllSeqAnnotations.setText(MessageManager
619 .getString("label.hide_all_seq_annotations"));
620 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
621 hideAllSeqAnnotations.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent e)
626 hideAllAnnotations_actionPerformed(true, false);
629 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
630 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
631 SequenceAnnotationOrder.NONE.name()));
632 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
633 MessageManager.getString("label.sort_annotations_by_sequence"));
634 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
635 MessageManager.getString("label.sort_annotations_by_label"));
638 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
639 sortAnnBySequence.addActionListener(new ActionListener()
642 public void actionPerformed(ActionEvent e)
644 boolean newState = sortAnnBySequence.getState();
645 sortAnnByLabel.setSelected(false);
646 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
647 : SequenceAnnotationOrder.NONE);
648 sortAnnotations_actionPerformed();
652 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
653 sortAnnByLabel.addActionListener(new ActionListener()
656 public void actionPerformed(ActionEvent e)
658 boolean newState = sortAnnByLabel.getState();
659 sortAnnBySequence.setSelected(false);
660 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
661 : SequenceAnnotationOrder.NONE);
662 sortAnnotations_actionPerformed();
665 colourTextMenuItem = new JCheckBoxMenuItem(
667 .getString("label.colour_text"));
668 colourTextMenuItem.addActionListener(new ActionListener()
671 public void actionPerformed(ActionEvent e)
673 colourTextMenuItem_actionPerformed(e);
677 JMenuItem htmlMenuItem = new JMenuItem(
678 MessageManager.getString("label.html"));
679 htmlMenuItem.addActionListener(new ActionListener()
682 public void actionPerformed(ActionEvent e)
684 htmlMenuItem_actionPerformed(e);
688 JMenuItem createBioJS = new JMenuItem(
689 MessageManager.getString("label.biojs_html_export"));
690 createBioJS.addActionListener(new java.awt.event.ActionListener()
693 public void actionPerformed(ActionEvent e)
695 bioJSMenuItem_actionPerformed(e);
699 JMenuItem overviewMenuItem = new JMenuItem(
700 MessageManager.getString("label.overview_window"));
701 overviewMenuItem.addActionListener(new ActionListener()
704 public void actionPerformed(ActionEvent e)
706 overviewMenuItem_actionPerformed(e);
710 undoMenuItem.setEnabled(false);
711 undoMenuItem.setText(MessageManager.getString("action.undo"));
712 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
713 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
714 al = new ActionListener()
717 public void actionPerformed(ActionEvent e)
719 undoMenuItem_actionPerformed(e);
722 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
724 redoMenuItem.setEnabled(false);
725 redoMenuItem.setText(MessageManager.getString("action.redo"));
726 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
727 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
728 al = new ActionListener()
731 public void actionPerformed(ActionEvent e)
733 redoMenuItem_actionPerformed(e);
736 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
738 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
739 wrapMenuItem.addActionListener(new ActionListener()
742 public void actionPerformed(ActionEvent e)
744 wrapMenuItem_actionPerformed(e);
748 JMenuItem printMenuItem = new JMenuItem(
749 MessageManager.getString("action.print"));
750 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
751 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
752 al = new ActionListener()
755 public void actionPerformed(ActionEvent e)
757 printMenuItem_actionPerformed(e);
760 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
763 .setText(MessageManager.getString("action.show_gaps"));
764 renderGapsMenuItem.setState(true);
765 renderGapsMenuItem.addActionListener(new ActionListener()
768 public void actionPerformed(ActionEvent e)
770 renderGapsMenuItem_actionPerformed(e);
774 JMenuItem findMenuItem = new JMenuItem(
775 MessageManager.getString("action.find"));
776 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
777 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
778 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
779 MessageManager.getString("label.find_tip")));
780 al = new ActionListener()
783 public void actionPerformed(ActionEvent e)
785 findMenuItem_actionPerformed(e);
788 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
790 showSeqFeatures.setText(MessageManager
791 .getString("label.show_sequence_features"));
792 showSeqFeatures.addActionListener(new ActionListener()
795 public void actionPerformed(ActionEvent actionEvent)
797 showSeqFeatures_actionPerformed(actionEvent);
801 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
802 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
803 * void actionPerformed(ActionEvent actionEvent) {
804 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
806 showDbRefsMenuitem.setText(MessageManager
807 .getString("label.show_database_refs"));
808 showDbRefsMenuitem.addActionListener(new ActionListener()
812 public void actionPerformed(ActionEvent e)
814 showDbRefs_actionPerformed(e);
818 showNpFeatsMenuitem.setText(MessageManager
819 .getString("label.show_non_positional_features"));
820 showNpFeatsMenuitem.addActionListener(new ActionListener()
824 public void actionPerformed(ActionEvent e)
826 showNpFeats_actionPerformed(e);
830 showGroupConservation.setText(MessageManager
831 .getString("label.group_conservation"));
832 showGroupConservation.addActionListener(new ActionListener()
836 public void actionPerformed(ActionEvent e)
838 showGroupConservation_actionPerformed(e);
843 showGroupConsensus.setText(MessageManager
844 .getString("label.group_consensus"));
845 showGroupConsensus.addActionListener(new ActionListener()
849 public void actionPerformed(ActionEvent e)
851 showGroupConsensus_actionPerformed(e);
855 showConsensusHistogram.setText(MessageManager
856 .getString("label.show_consensus_histogram"));
857 showConsensusHistogram.addActionListener(new ActionListener()
861 public void actionPerformed(ActionEvent e)
863 showConsensusHistogram_actionPerformed(e);
867 showSequenceLogo.setText(MessageManager
868 .getString("label.show_consensus_logo"));
869 showSequenceLogo.addActionListener(new ActionListener()
873 public void actionPerformed(ActionEvent e)
875 showSequenceLogo_actionPerformed(e);
879 normaliseSequenceLogo.setText(MessageManager
880 .getString("label.norm_consensus_logo"));
881 normaliseSequenceLogo.addActionListener(new ActionListener()
885 public void actionPerformed(ActionEvent e)
887 normaliseSequenceLogo_actionPerformed(e);
891 applyAutoAnnotationSettings.setText(MessageManager
892 .getString("label.apply_all_groups"));
893 applyAutoAnnotationSettings.setState(false);
894 applyAutoAnnotationSettings.setVisible(true);
895 applyAutoAnnotationSettings.addActionListener(new ActionListener()
898 public void actionPerformed(ActionEvent e)
900 applyAutoAnnotationSettings_actionPerformed(e);
904 ButtonGroup buttonGroup = new ButtonGroup();
905 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
906 MessageManager.getString("label.show_first"));
907 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
908 MessageManager.getString("label.show_last"));
909 buttonGroup.add(showAutoFirst);
910 buttonGroup.add(showAutoLast);
911 final boolean autoFirst = Cache.getDefault(
912 Preferences.SHOW_AUTOCALC_ABOVE, false);
913 showAutoFirst.setSelected(autoFirst);
914 setShowAutoCalculatedAbove(autoFirst);
915 showAutoFirst.addActionListener(new ActionListener()
918 public void actionPerformed(ActionEvent e)
920 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
921 sortAnnotations_actionPerformed();
924 showAutoLast.setSelected(!showAutoFirst.isSelected());
925 showAutoLast.addActionListener(new ActionListener()
928 public void actionPerformed(ActionEvent e)
930 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
931 sortAnnotations_actionPerformed();
935 JMenuItem deleteGroups = new JMenuItem(
936 MessageManager.getString("action.undefine_groups"));
937 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
938 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
939 al = new ActionListener()
942 public void actionPerformed(ActionEvent e)
944 deleteGroups_actionPerformed(e);
947 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
949 JMenuItem annotationColumn = new JMenuItem(
950 MessageManager.getString("action.select_by_annotation"));
951 annotationColumn.addActionListener(new ActionListener()
954 public void actionPerformed(ActionEvent e)
956 annotationColumn_actionPerformed(e);
960 JMenuItem createGroup = new JMenuItem(
961 MessageManager.getString("action.create_group"));
962 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
963 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
964 al = new ActionListener()
967 public void actionPerformed(ActionEvent e)
969 createGroup_actionPerformed(e);
972 addMenuActionAndAccelerator(keyStroke, createGroup, al);
974 JMenuItem unGroup = new JMenuItem(
975 MessageManager.getString("action.remove_group"));
976 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
977 .getDefaultToolkit().getMenuShortcutKeyMask()
978 | KeyEvent.SHIFT_MASK, false);
979 al = new ActionListener()
982 public void actionPerformed(ActionEvent e)
984 unGroup_actionPerformed(e);
987 addMenuActionAndAccelerator(keyStroke, unGroup, al);
989 copy.setText(MessageManager.getString("action.copy"));
990 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
991 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
993 al = new ActionListener()
996 public void actionPerformed(ActionEvent e)
998 copy_actionPerformed(e);
1001 addMenuActionAndAccelerator(keyStroke, copy, al);
1003 cut.setText(MessageManager.getString("action.cut"));
1004 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1005 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1006 al = new ActionListener()
1009 public void actionPerformed(ActionEvent e)
1011 cut_actionPerformed(e);
1014 addMenuActionAndAccelerator(keyStroke, cut, al);
1016 JMenuItem delete = new JMenuItem(
1017 MessageManager.getString("action.delete"));
1018 delete.addActionListener(new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 delete_actionPerformed(e);
1027 pasteMenu.setText(MessageManager.getString("action.paste"));
1028 JMenuItem pasteNew = new JMenuItem(
1029 MessageManager.getString("label.to_new_alignment"));
1030 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1031 .getDefaultToolkit().getMenuShortcutKeyMask()
1032 | KeyEvent.SHIFT_MASK, false);
1033 al = new ActionListener()
1036 public void actionPerformed(ActionEvent e)
1040 pasteNew_actionPerformed(e);
1041 } catch (IOException | InterruptedException e1)
1043 // TODO Auto-generated catch block
1044 e1.printStackTrace();
1048 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1050 JMenuItem pasteThis = new JMenuItem(
1051 MessageManager.getString("label.to_this_alignment"));
1052 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1053 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1054 al = new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1061 pasteThis_actionPerformed(e);
1062 } catch (IOException | InterruptedException e1)
1064 // TODO Auto-generated catch block
1065 e1.printStackTrace();
1069 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1071 JMenuItem createPNG = new JMenuItem("PNG");
1072 createPNG.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1080 createPNG.setActionCommand(MessageManager
1081 .getString("label.save_png_image"));
1083 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1084 font.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1089 font_actionPerformed(e);
1092 seqLimits.setText(MessageManager
1093 .getString("label.show_sequence_limits"));
1094 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1095 seqLimits.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 seqLimit_actionPerformed(e);
1103 JMenuItem epsFile = new JMenuItem("EPS");
1104 epsFile.addActionListener(new ActionListener()
1107 public void actionPerformed(ActionEvent e)
1113 JMenuItem createSVG = new JMenuItem("SVG");
1114 createSVG.addActionListener(new ActionListener()
1117 public void actionPerformed(ActionEvent e)
1123 JMenuItem loadTreeMenuItem = new JMenuItem(
1124 MessageManager.getString("label.load_associated_tree"));
1125 loadTreeMenuItem.setActionCommand(MessageManager
1126 .getString("label.load_tree_for_sequence_set"));
1127 loadTreeMenuItem.addActionListener(new ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 loadTreeMenuItem_actionPerformed(e);
1136 scaleAbove.setVisible(false);
1137 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1138 scaleAbove.addActionListener(new ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 scaleAbove_actionPerformed(e);
1146 scaleLeft.setVisible(false);
1147 scaleLeft.setSelected(true);
1148 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1149 scaleLeft.addActionListener(new ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 scaleLeft_actionPerformed(e);
1157 scaleRight.setVisible(false);
1158 scaleRight.setSelected(true);
1159 scaleRight.setText(MessageManager.getString("action.scale_right"));
1160 scaleRight.addActionListener(new ActionListener()
1163 public void actionPerformed(ActionEvent e)
1165 scaleRight_actionPerformed(e);
1168 centreColumnLabelsMenuItem.setVisible(true);
1169 centreColumnLabelsMenuItem.setState(false);
1170 centreColumnLabelsMenuItem.setText(MessageManager
1171 .getString("label.centre_column_labels"));
1172 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 centreColumnLabels_actionPerformed(e);
1180 followHighlightMenuItem.setVisible(true);
1181 followHighlightMenuItem.setState(true);
1182 followHighlightMenuItem.setText(MessageManager
1183 .getString("label.automatic_scrolling"));
1184 followHighlightMenuItem.addActionListener(new ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 followHighlight_actionPerformed();
1196 .setText(MessageManager.getString("action.by_tree_order"));
1197 sort.setText(MessageManager.getString("action.sort"));
1198 sort.addMenuListener(new MenuListener()
1201 public void menuSelected(MenuEvent e)
1203 buildTreeSortMenu();
1207 public void menuDeselected(MenuEvent e)
1212 public void menuCanceled(MenuEvent e)
1216 sortByAnnotScore.setText(MessageManager
1217 .getString("label.sort_by_score"));
1218 sort.add(sortByAnnotScore);
1219 sort.addMenuListener(new javax.swing.event.MenuListener()
1223 public void menuCanceled(MenuEvent e)
1228 public void menuDeselected(MenuEvent e)
1233 public void menuSelected(MenuEvent e)
1235 buildSortByAnnotationScoresMenu();
1238 sortByAnnotScore.setVisible(false);
1240 calculateTree.setText(MessageManager
1241 .getString("action.calculate_tree_pca"));
1243 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1244 padGapsMenuitem.setState(jalview.bin.Cache
1245 .getDefault("PAD_GAPS", false));
1246 padGapsMenuitem.addActionListener(new ActionListener()
1249 public void actionPerformed(ActionEvent e)
1251 padGapsMenuitem_actionPerformed(e);
1254 JMenuItem vamsasStore = new JMenuItem(
1255 MessageManager.getString("label.vamsas_store"));
1256 vamsasStore.setVisible(false);
1257 vamsasStore.addActionListener(new ActionListener()
1260 public void actionPerformed(ActionEvent e)
1262 vamsasStore_actionPerformed(e);
1265 showTranslation.setText(MessageManager
1266 .getString("label.translate_cDNA"));
1267 showTranslation.addActionListener(new ActionListener()
1270 public void actionPerformed(ActionEvent e)
1272 showTranslation_actionPerformed(e);
1275 showReverse.setText(MessageManager.getString("label.reverse"));
1276 showReverse.addActionListener(new ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 showReverse_actionPerformed(false);
1284 showReverseComplement.setText(MessageManager
1285 .getString("label.reverse_complement"));
1286 showReverseComplement.addActionListener(new ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 showReverse_actionPerformed(true);
1295 JMenuItem extractScores = new JMenuItem(
1296 MessageManager.getString("label.extract_scores"));
1297 extractScores.addActionListener(new ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 extractScores_actionPerformed(e);
1305 extractScores.setVisible(true);
1306 // JBPNote: TODO: make gui for regex based score extraction
1308 // for show products actions see AlignFrame.canShowProducts
1309 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1311 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1312 runGroovy.setToolTipText(MessageManager
1313 .getString("label.run_groovy_tip"));
1314 runGroovy.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent e)
1319 runGroovy_actionPerformed();
1323 JMenuItem openFeatureSettings = new JMenuItem(
1324 MessageManager.getString("action.feature_settings"));
1325 openFeatureSettings.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 featureSettings_actionPerformed(e);
1333 JMenuItem fetchSequence = new JMenuItem(
1334 MessageManager.getString("label.fetch_sequences"));
1335 fetchSequence.addActionListener(new ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 fetchSequence_actionPerformed(e);
1344 JMenuItem associatedData = new JMenuItem(
1345 MessageManager.getString("label.load_features_annotations"));
1346 associatedData.addActionListener(new ActionListener()
1349 public void actionPerformed(ActionEvent e)
1353 associatedData_actionPerformed(e);
1354 } catch (IOException | InterruptedException e1)
1356 // TODO Auto-generated catch block
1357 e1.printStackTrace();
1361 autoCalculate.setText(MessageManager
1362 .getString("label.autocalculate_consensus"));
1363 autoCalculate.setState(jalview.bin.Cache.getDefault(
1364 "AUTO_CALC_CONSENSUS", true));
1365 autoCalculate.addActionListener(new ActionListener()
1368 public void actionPerformed(ActionEvent e)
1370 autoCalculate_actionPerformed(e);
1373 sortByTree.setText(MessageManager
1374 .getString("label.sort_alignment_new_tree"));
1376 .setToolTipText("<html>"
1378 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1380 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1381 sortByTree.addActionListener(new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 sortByTreeOption_actionPerformed(e);
1390 listenToViewSelections.setText(MessageManager
1391 .getString("label.listen_for_selections"));
1392 listenToViewSelections
1393 .setToolTipText("<html>"
1395 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1396 listenToViewSelections.setState(false);
1397 listenToViewSelections.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 listenToViewSelections_actionPerformed(e);
1406 JMenu addSequenceMenu = new JMenu(
1407 MessageManager.getString("label.add_sequences"));
1408 JMenuItem addFromFile = new JMenuItem(
1409 MessageManager.getString("label.from_file"));
1410 addFromFile.addActionListener(new ActionListener()
1413 public void actionPerformed(ActionEvent e)
1415 addFromFile_actionPerformed(e);
1418 JMenuItem addFromText = new JMenuItem(
1419 MessageManager.getString("label.from_textbox"));
1420 addFromText.addActionListener(new ActionListener()
1423 public void actionPerformed(ActionEvent e)
1425 addFromText_actionPerformed(e);
1428 JMenuItem addFromURL = new JMenuItem(
1429 MessageManager.getString("label.from_url"));
1430 addFromURL.addActionListener(new ActionListener()
1433 public void actionPerformed(ActionEvent e)
1435 addFromURL_actionPerformed(e);
1438 JMenuItem exportFeatures = new JMenuItem(
1439 MessageManager.getString("label.export_features"));
1440 exportFeatures.addActionListener(new ActionListener()
1443 public void actionPerformed(ActionEvent e)
1445 exportFeatures_actionPerformed(e);
1448 JMenuItem exportAnnotations = new JMenuItem(
1449 MessageManager.getString("label.export_annotations"));
1450 exportAnnotations.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 exportAnnotations_actionPerformed(e);
1458 statusPanel.setLayout(new GridLayout());
1459 JMenuItem showAllSeqs = new JMenuItem(
1460 MessageManager.getString("label.all_sequences"));
1461 showAllSeqs.setToolTipText(MessageManager
1462 .getString("label.toggle_sequence_visibility"));
1463 showAllSeqs.addActionListener(new ActionListener()
1466 public void actionPerformed(ActionEvent e)
1468 showAllSeqs_actionPerformed(e);
1471 JMenuItem showAllColumns = new JMenuItem(
1472 MessageManager.getString("label.all_columns"));
1473 showAllColumns.setToolTipText(MessageManager
1474 .getString("label.toggle_columns_visibility"));
1475 showAllColumns.addActionListener(new ActionListener()
1478 public void actionPerformed(ActionEvent e)
1480 showAllColumns_actionPerformed(e);
1483 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1484 JMenuItem hideSelSequences = new JMenuItem(
1485 MessageManager.getString("label.selected_sequences"));
1486 hideSelSequences.setToolTipText(MessageManager
1487 .getString("label.toggle_sequence_visibility"));
1488 hideSelSequences.addActionListener(new ActionListener()
1491 public void actionPerformed(ActionEvent e)
1493 hideSelSequences_actionPerformed(e);
1496 JMenuItem hideSelColumns = new JMenuItem(
1497 MessageManager.getString("label.selected_columns"));
1498 hideSelColumns.setToolTipText(MessageManager
1499 .getString("label.toggle_columns_visibility"));
1500 hideSelColumns.addActionListener(new ActionListener()
1503 public void actionPerformed(ActionEvent e)
1505 hideSelColumns_actionPerformed(e);
1508 JMenuItem hideAllSelection = new JMenuItem(
1509 MessageManager.getString("label.selected_region"));
1510 hideAllSelection.addActionListener(new ActionListener()
1513 public void actionPerformed(ActionEvent e)
1515 hideAllSelection_actionPerformed(e);
1518 // TODO: should be hidden if no selection exists.
1519 JMenuItem hideAllButSelection = new JMenuItem(
1520 MessageManager.getString("label.all_but_selected_region"));
1521 hideAllButSelection.addActionListener(new ActionListener()
1524 public void actionPerformed(ActionEvent e)
1526 hideAllButSelection_actionPerformed(e);
1529 JMenuItem showAllhidden = new JMenuItem(
1530 MessageManager.getString("label.all_sequences_columns"));
1531 showAllhidden.setToolTipText(MessageManager
1532 .getString("label.toggles_visibility_hidden_selected_regions"));
1533 showAllhidden.addActionListener(new ActionListener()
1536 public void actionPerformed(ActionEvent e)
1538 showAllhidden_actionPerformed(e);
1541 hiddenMarkers.setText(MessageManager
1542 .getString("action.show_hidden_markers"));
1543 hiddenMarkers.addActionListener(new ActionListener()
1546 public void actionPerformed(ActionEvent e)
1548 hiddenMarkers_actionPerformed(e);
1552 JMenuItem invertColSel = new JMenuItem(
1553 MessageManager.getString("action.invert_column_selection"));
1554 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1555 .getDefaultToolkit().getMenuShortcutKeyMask()
1556 | KeyEvent.ALT_MASK, false);
1557 al = new ActionListener()
1560 public void actionPerformed(ActionEvent e)
1562 invertColSel_actionPerformed(e);
1565 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1567 showComplementMenuItem.setVisible(false);
1568 showComplementMenuItem.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 showComplement_actionPerformed(showComplementMenuItem.getState());
1577 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1580 public void stateChanged(ChangeEvent evt)
1582 JTabbedPane pane = (JTabbedPane) evt.getSource();
1583 int sel = pane.getSelectedIndex();
1584 tabSelectionChanged(sel);
1587 tabbedPane.addMouseListener(new MouseAdapter()
1590 public void mousePressed(MouseEvent e)
1592 if (e.isPopupTrigger()) // Mac
1594 tabbedPane_mousePressed(e);
1599 public void mouseReleased(MouseEvent e)
1601 if (e.isPopupTrigger()) // Windows
1603 tabbedPane_mousePressed(e);
1607 tabbedPane.addFocusListener(new FocusAdapter()
1610 public void focusGained(FocusEvent e)
1612 tabbedPane_focusGained(e);
1616 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1617 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1618 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1619 al = new ActionListener()
1622 public void actionPerformed(ActionEvent e)
1624 save_actionPerformed(e);
1627 addMenuActionAndAccelerator(keyStroke, save, al);
1629 reload.setEnabled(false);
1630 reload.setText(MessageManager.getString("action.reload"));
1631 reload.addActionListener(new ActionListener()
1634 public void actionPerformed(ActionEvent e)
1636 reload_actionPerformed(e);
1640 JMenuItem newView = new JMenuItem(
1641 MessageManager.getString("action.new_view"));
1642 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1643 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1644 al = new ActionListener()
1647 public void actionPerformed(ActionEvent e)
1649 newView_actionPerformed(e);
1652 addMenuActionAndAccelerator(keyStroke, newView, al);
1654 tabbedPane.setToolTipText("<html><i>"
1655 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1658 formatMenu.setText(MessageManager.getString("action.format"));
1659 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1661 idRightAlign.setText(MessageManager
1662 .getString("label.right_align_sequence_id"));
1663 idRightAlign.addActionListener(new ActionListener()
1666 public void actionPerformed(ActionEvent e)
1668 idRightAlign_actionPerformed(e);
1672 gatherViews.setEnabled(false);
1673 gatherViews.setText(MessageManager.getString("action.gather_views"));
1674 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1675 al = new ActionListener()
1678 public void actionPerformed(ActionEvent e)
1680 gatherViews_actionPerformed(e);
1683 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1685 expandViews.setEnabled(false);
1686 expandViews.setText(MessageManager.getString("action.expand_views"));
1687 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1688 al = new ActionListener()
1691 public void actionPerformed(ActionEvent e)
1693 expandViews_actionPerformed(e);
1696 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1698 JMenuItem pageSetup = new JMenuItem(
1699 MessageManager.getString("action.page_setup"));
1700 pageSetup.addActionListener(new ActionListener()
1703 public void actionPerformed(ActionEvent e)
1705 pageSetup_actionPerformed(e);
1708 JMenuItem alignmentProperties = new JMenuItem(
1709 MessageManager.getString("label.alignment_props"));
1710 alignmentProperties.addActionListener(new ActionListener()
1713 public void actionPerformed(ActionEvent actionEvent)
1715 alignmentProperties();
1718 JMenuItem selectHighlighted = new JMenuItem(
1719 MessageManager.getString("action.select_highlighted_columns"));
1720 selectHighlighted.setToolTipText(MessageManager
1721 .getString("tooltip.select_highlighted_columns"));
1722 al = new ActionListener()
1725 public void actionPerformed(ActionEvent actionEvent)
1727 selectHighlightedColumns_actionPerformed(actionEvent);
1730 hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
1731 hmmBuild.addActionListener(new ActionListener()
1735 public void actionPerformed(ActionEvent e)
1739 hmmBuild_actionPerformed(e);
1740 } catch (IOException e1)
1742 // TODO Auto-generated catch block
1743 e1.printStackTrace();
1744 } catch (InterruptedException e1)
1746 // TODO Auto-generated catch block
1747 e1.printStackTrace();
1752 hmmAlign.setText(MessageManager.getString("label.hmmalign"));
1753 hmmAlign.addActionListener(new ActionListener()
1757 public void actionPerformed(ActionEvent e)
1761 hmmAlign_actionPerformed(e);
1762 } catch (IOException e1)
1764 // TODO Auto-generated catch block
1765 e1.printStackTrace();
1766 } catch (InterruptedException e1)
1768 // TODO Auto-generated catch block
1769 e1.printStackTrace();
1774 selectHighlighted.addActionListener(al);
1775 JMenu tooltipSettingsMenu = new JMenu(
1776 MessageManager.getString("label.sequence_id_tooltip"));
1777 JMenu autoAnnMenu = new JMenu(
1778 MessageManager.getString("label.autocalculated_annotation"));
1780 JMenu exportImageMenu = new JMenu(
1781 MessageManager.getString("label.export_image"));
1782 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1783 alignFrameMenuBar.add(fileMenu);
1784 alignFrameMenuBar.add(editMenu);
1785 alignFrameMenuBar.add(selectMenu);
1786 alignFrameMenuBar.add(viewMenu);
1787 alignFrameMenuBar.add(annotationsMenu);
1788 alignFrameMenuBar.add(formatMenu);
1789 alignFrameMenuBar.add(colourMenu);
1790 alignFrameMenuBar.add(calculateMenu);
1791 alignFrameMenuBar.add(webService);
1792 alignFrameMenuBar.add(hmmerMenu);
1794 fileMenu.add(fetchSequence);
1795 fileMenu.add(addSequenceMenu);
1796 fileMenu.add(reload);
1797 fileMenu.addSeparator();
1798 fileMenu.add(vamsasStore);
1800 fileMenu.add(saveAs);
1801 fileMenu.add(outputTextboxMenu);
1802 fileMenu.add(pageSetup);
1803 fileMenu.add(printMenuItem);
1804 fileMenu.addSeparator();
1805 fileMenu.add(exportImageMenu);
1806 fileMenu.add(exportFeatures);
1807 fileMenu.add(exportAnnotations);
1808 fileMenu.add(loadTreeMenuItem);
1809 fileMenu.add(associatedData);
1810 fileMenu.addSeparator();
1811 fileMenu.add(closeMenuItem);
1813 pasteMenu.add(pasteNew);
1814 pasteMenu.add(pasteThis);
1815 editMenu.add(undoMenuItem);
1816 editMenu.add(redoMenuItem);
1819 editMenu.add(pasteMenu);
1820 editMenu.add(delete);
1821 editMenu.addSeparator();
1822 editMenu.add(remove2LeftMenuItem);
1823 editMenu.add(remove2RightMenuItem);
1824 editMenu.add(removeGappedColumnMenuItem);
1825 editMenu.add(removeAllGapsMenuItem);
1826 editMenu.add(removeRedundancyMenuItem);
1827 editMenu.addSeparator();
1828 // dont add these yet in the CVS build - they cannot be undone!
1829 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1830 // editMenu.add(justifyLeftMenuItem);
1831 // editMenu.add(justifyRightMenuItem);
1832 // editMenu.addSeparator();
1833 editMenu.add(padGapsMenuitem);
1835 showMenu.add(showAllColumns);
1836 showMenu.add(showAllSeqs);
1837 showMenu.add(showAllhidden);
1838 hideMenu.add(hideSelColumns);
1839 hideMenu.add(hideSelSequences);
1840 hideMenu.add(hideAllSelection);
1841 hideMenu.add(hideAllButSelection);
1842 viewMenu.add(newView);
1843 viewMenu.add(expandViews);
1844 viewMenu.add(gatherViews);
1845 viewMenu.addSeparator();
1846 viewMenu.add(showMenu);
1847 viewMenu.add(hideMenu);
1848 viewMenu.add(showComplementMenuItem);
1849 viewMenu.addSeparator();
1850 viewMenu.add(followHighlightMenuItem);
1851 viewMenu.addSeparator();
1852 viewMenu.add(showSeqFeatures);
1853 // viewMenu.add(showSeqFeaturesHeight);
1854 viewMenu.add(openFeatureSettings);
1855 tooltipSettingsMenu.add(showDbRefsMenuitem);
1856 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1857 viewMenu.add(tooltipSettingsMenu);
1858 viewMenu.addSeparator();
1859 viewMenu.add(alignmentProperties);
1860 viewMenu.addSeparator();
1861 viewMenu.add(overviewMenuItem);
1863 annotationsMenu.add(annotationPanelMenuItem);
1864 annotationsMenu.addSeparator();
1865 annotationsMenu.add(showAllAlAnnotations);
1866 annotationsMenu.add(hideAllAlAnnotations);
1867 annotationsMenu.addSeparator();
1868 annotationsMenu.add(showAllSeqAnnotations);
1869 annotationsMenu.add(hideAllSeqAnnotations);
1870 annotationsMenu.add(sortAnnBySequence);
1871 annotationsMenu.add(sortAnnByLabel);
1872 annotationsMenu.addSeparator();
1873 autoAnnMenu.add(showAutoFirst);
1874 autoAnnMenu.add(showAutoLast);
1875 autoAnnMenu.addSeparator();
1876 autoAnnMenu.add(applyAutoAnnotationSettings);
1877 autoAnnMenu.add(showConsensusHistogram);
1878 autoAnnMenu.add(showSequenceLogo);
1879 autoAnnMenu.add(normaliseSequenceLogo);
1880 autoAnnMenu.addSeparator();
1881 autoAnnMenu.add(showGroupConservation);
1882 autoAnnMenu.add(showGroupConsensus);
1883 annotationsMenu.add(autoAnnMenu);
1886 sort.add(sortIDMenuItem);
1887 sort.add(sortLengthMenuItem);
1888 sort.add(sortGroupMenuItem);
1889 sort.add(sortPairwiseMenuItem);
1890 sort.add(sortByTreeMenu);
1891 calculateMenu.add(sort);
1892 calculateMenu.add(calculateTree);
1893 calculateMenu.addSeparator();
1894 calculateMenu.add(pairwiseAlignmentMenuItem);
1895 calculateMenu.addSeparator();
1896 calculateMenu.add(showTranslation);
1897 calculateMenu.add(showReverse);
1898 calculateMenu.add(showReverseComplement);
1899 calculateMenu.add(showProducts);
1900 calculateMenu.add(autoCalculate);
1901 calculateMenu.add(sortByTree);
1902 calculateMenu.addSeparator();
1903 calculateMenu.add(expandAlignment);
1904 calculateMenu.add(extractScores);
1905 calculateMenu.addSeparator();
1906 calculateMenu.add(runGroovy);
1908 webServiceNoServices = new JMenuItem(
1909 MessageManager.getString("label.no_services"));
1910 webService.add(webServiceNoServices);
1911 exportImageMenu.add(htmlMenuItem);
1912 exportImageMenu.add(epsFile);
1913 exportImageMenu.add(createPNG);
1914 exportImageMenu.add(createBioJS);
1915 exportImageMenu.add(createSVG);
1916 addSequenceMenu.add(addFromFile);
1917 addSequenceMenu.add(addFromText);
1918 addSequenceMenu.add(addFromURL);
1919 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1920 statusPanel.add(statusBar, null);
1921 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1923 formatMenu.add(font);
1924 formatMenu.addSeparator();
1925 formatMenu.add(wrapMenuItem);
1926 formatMenu.add(scaleAbove);
1927 formatMenu.add(scaleLeft);
1928 formatMenu.add(scaleRight);
1929 formatMenu.add(seqLimits);
1930 formatMenu.add(idRightAlign);
1931 formatMenu.add(hiddenMarkers);
1932 formatMenu.add(viewBoxesMenuItem);
1933 formatMenu.add(viewTextMenuItem);
1934 formatMenu.add(colourTextMenuItem);
1935 formatMenu.add(renderGapsMenuItem);
1936 formatMenu.add(centreColumnLabelsMenuItem);
1937 formatMenu.add(showNonconservedMenuItem);
1938 selectMenu.add(findMenuItem);
1939 selectMenu.addSeparator();
1940 selectMenu.add(selectAllSequenceMenuItem);
1941 selectMenu.add(deselectAllSequenceMenuItem);
1942 selectMenu.add(invertSequenceMenuItem);
1943 selectMenu.add(invertColSel);
1944 selectMenu.add(createGroup);
1945 selectMenu.add(unGroup);
1946 selectMenu.add(grpsFromSelection);
1947 selectMenu.add(deleteGroups);
1948 selectMenu.add(annotationColumn);
1949 selectMenu.add(selectHighlighted);
1950 // TODO - determine if the listenToViewSelections button is needed : see bug
1952 // selectMenu.addSeparator();
1953 // selectMenu.add(listenToViewSelections);
1956 public void hmmerMenu_actionPerformed(ActionEvent e)
1962 * Constructs the entries on the Colour menu (but does not add them to the
1965 protected void initHMMERMenu()
1967 hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
1968 hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
1969 hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
1971 protected void initColourMenu()
1973 applyToAllGroups = new JCheckBoxMenuItem(
1974 MessageManager.getString("label.apply_colour_to_all_groups"));
1975 applyToAllGroups.addActionListener(new ActionListener()
1978 public void actionPerformed(ActionEvent e)
1980 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1984 textColour = new JMenuItem(
1985 MessageManager.getString("label.text_colour"));
1986 textColour.addActionListener(new ActionListener()
1989 public void actionPerformed(ActionEvent e)
1991 textColour_actionPerformed();
1995 conservationMenuItem = new JCheckBoxMenuItem(
1996 MessageManager.getString("action.by_conservation"));
1997 conservationMenuItem.addActionListener(new ActionListener()
2000 public void actionPerformed(ActionEvent e)
2002 conservationMenuItem_actionPerformed(conservationMenuItem
2007 abovePIDThreshold = new JCheckBoxMenuItem(
2008 MessageManager.getString("label.above_identity_threshold"));
2009 abovePIDThreshold.addActionListener(new ActionListener()
2012 public void actionPerformed(ActionEvent e)
2014 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2017 modifyPID = new JMenuItem(
2018 MessageManager.getString("label.modify_identity_threshold"));
2019 modifyPID.addActionListener(new ActionListener()
2022 public void actionPerformed(ActionEvent e)
2024 modifyPID_actionPerformed();
2027 modifyConservation = new JMenuItem(
2029 .getString("label.modify_conservation_threshold"));
2030 modifyConservation.addActionListener(new ActionListener()
2033 public void actionPerformed(ActionEvent e)
2035 modifyConservation_actionPerformed();
2039 annotationColour = new JMenuItem(
2040 MessageManager.getString("action.by_annotation"));
2041 annotationColour.addActionListener(new ActionListener()
2044 public void actionPerformed(ActionEvent e)
2046 annotationColour_actionPerformed();
2051 protected void selectHighlightedColumns_actionPerformed(
2052 ActionEvent actionEvent)
2054 // TODO Auto-generated method stub
2059 * Generate the reverse sequence (or reverse complement if the flag is true)
2060 * and add it to the alignment
2064 protected void showReverse_actionPerformed(boolean complement)
2069 * Try to run script in a Groovy console, having first ensured that this
2070 * alignframe is set as currentAlignFrame in Desktop
2072 protected void runGroovy_actionPerformed()
2078 * Adds the given action listener and key accelerator to the given menu item.
2079 * Also saves in a lookup table to support lookup of action by key stroke.
2083 * @param actionListener
2085 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2086 JMenuItem menuItem, ActionListener actionListener)
2088 menuItem.setAccelerator(keyStroke);
2089 accelerators.put(keyStroke, menuItem);
2090 menuItem.addActionListener(actionListener);
2094 * Action on clicking sort annotations by type.
2098 protected void sortAnnotations_actionPerformed()
2103 * Action on clicking Show all annotations.
2105 * @param forSequences
2106 * update sequence-related annotations
2107 * @param forAlignment
2108 * update non-sequence-related annotations
2110 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2111 boolean forAlignment)
2113 setAnnotationsVisibility(true, forSequences, forAlignment);
2117 * Action on clicking Hide all annotations.
2119 * @param forSequences
2120 * update sequence-related annotations
2121 * @param forAlignment
2122 * update non-sequence-related annotations
2124 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2125 boolean forAlignment)
2127 setAnnotationsVisibility(false, forSequences, forAlignment);
2131 * Set the visibility of annotations to true or false. Can act on
2132 * sequence-related annotations, or alignment-related, or both.
2135 * @param forSequences
2136 * update sequence-related annotations
2137 * @param forAlignment
2138 * update non-sequence-related annotations
2140 protected void setAnnotationsVisibility(boolean visible,
2141 boolean forSequences, boolean forAlignment)
2146 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2148 // TODO Auto-generated method stub
2152 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2154 // TODO Auto-generated method stub
2158 protected void showAllhidden_actionPerformed(ActionEvent e)
2160 // TODO Auto-generated method stub
2164 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2166 // TODO Auto-generated method stub
2170 protected void hideAllSelection_actionPerformed(ActionEvent e)
2172 // TODO Auto-generated method stub
2176 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2178 // TODO Auto-generated method stub
2182 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2184 // TODO Auto-generated method stub
2188 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2190 // TODO Auto-generated method stub
2194 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2196 // TODO Auto-generated method stub
2200 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2202 // TODO Auto-generated method stub
2206 protected void showGroupConservation_actionPerformed(ActionEvent e)
2208 // TODO Auto-generated method stub
2212 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2214 // TODO Auto-generated method stub
2218 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2220 // TODO Auto-generated method stub
2224 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2226 // TODO Auto-generated method stub
2230 protected void followHighlight_actionPerformed()
2232 // TODO Auto-generated method stub
2236 protected void showNpFeats_actionPerformed(ActionEvent e)
2238 // TODO Auto-generated method stub
2242 protected void showDbRefs_actionPerformed(ActionEvent e)
2244 // TODO Auto-generated method stub
2248 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2252 protected void buildSortByAnnotationScoresMenu()
2256 protected void extractScores_actionPerformed(ActionEvent e)
2260 protected void outputText_actionPerformed(ActionEvent e)
2264 public void addFromFile_actionPerformed(ActionEvent e)
2269 public void addFromText_actionPerformed(ActionEvent e)
2274 public void addFromURL_actionPerformed(ActionEvent e)
2279 public void exportFeatures_actionPerformed(ActionEvent e)
2284 public void exportAnnotations_actionPerformed(ActionEvent e)
2289 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2293 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2298 protected void closeMenuItem_actionPerformed(boolean b)
2302 protected void redoMenuItem_actionPerformed(ActionEvent e)
2306 protected void undoMenuItem_actionPerformed(ActionEvent e)
2310 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2314 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2318 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2322 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2326 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2330 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2334 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2338 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2342 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2346 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2350 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2354 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2358 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2362 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2366 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2370 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2374 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2378 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2382 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2386 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2390 protected void conservationMenuItem_actionPerformed(boolean selected)
2394 protected void printMenuItem_actionPerformed(ActionEvent e)
2398 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2402 protected void findMenuItem_actionPerformed(ActionEvent e)
2406 protected void abovePIDThreshold_actionPerformed(boolean selected)
2410 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2414 protected void deleteGroups_actionPerformed(ActionEvent e)
2418 protected void createGroup_actionPerformed(ActionEvent e)
2422 protected void unGroup_actionPerformed(ActionEvent e)
2426 protected void copy_actionPerformed(ActionEvent e)
2430 protected void cut_actionPerformed(ActionEvent e)
2434 protected void delete_actionPerformed(ActionEvent e)
2438 protected void pasteNew_actionPerformed(ActionEvent e)
2439 throws IOException, InterruptedException
2443 protected void pasteThis_actionPerformed(ActionEvent e)
2444 throws IOException, InterruptedException
2448 protected void applyToAllGroups_actionPerformed(boolean selected)
2452 protected void autoAlignSeqs_actionPerformed(boolean selected)
2456 protected void hmmAlign_actionPerformed(ActionEvent e)
2457 throws IOException, InterruptedException
2461 protected void changeHMMERLocation_actionPerformed(ActionEvent e)
2465 protected void hmmBuild_actionPerformed(ActionEvent e)
2466 throws IOException, InterruptedException
2470 protected void hmmSearch_actionPerformed(ActionEvent e)
2474 public void createPNG(java.io.File f)
2478 protected void font_actionPerformed(ActionEvent e)
2482 protected void seqLimit_actionPerformed(ActionEvent e)
2486 public void seqDBRef_actionPerformed(ActionEvent e)
2491 public void createEPS(java.io.File f)
2495 public void createSVG(java.io.File f)
2500 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2506 * Template method to handle the 'load T-Coffee scores' menu event.
2508 * Subclasses override this method to provide a custom action.
2513 protected void loadScores_actionPerformed(ActionEvent event)
2518 protected void jpred_actionPerformed(ActionEvent e)
2522 protected void scaleAbove_actionPerformed(ActionEvent e)
2526 protected void scaleLeft_actionPerformed(ActionEvent e)
2530 protected void scaleRight_actionPerformed(ActionEvent e)
2534 protected void modifyPID_actionPerformed()
2538 protected void modifyConservation_actionPerformed()
2542 protected void saveAs_actionPerformed(ActionEvent e)
2546 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2550 public void vamsasStore_actionPerformed(ActionEvent e)
2555 public void vamsasLoad_actionPerformed(ActionEvent e)
2560 public void showTranslation_actionPerformed(ActionEvent e)
2565 public void featureSettings_actionPerformed(ActionEvent e)
2570 public void fetchSequence_actionPerformed(ActionEvent e)
2575 public void smoothFont_actionPerformed(ActionEvent e)
2580 public void annotationColour_actionPerformed()
2584 public void annotationColumn_actionPerformed(ActionEvent e)
2588 public void associatedData_actionPerformed(ActionEvent e)
2589 throws IOException, InterruptedException
2594 public void autoCalculate_actionPerformed(ActionEvent e)
2599 public void sortByTreeOption_actionPerformed(ActionEvent e)
2604 public void showAllSeqs_actionPerformed(ActionEvent e)
2609 public void showAllColumns_actionPerformed(ActionEvent e)
2614 public void hideSelSequences_actionPerformed(ActionEvent e)
2619 public void hideSelColumns_actionPerformed(ActionEvent e)
2624 public void hiddenMarkers_actionPerformed(ActionEvent e)
2629 public void findPdbId_actionPerformed(ActionEvent e)
2634 public void enterPdbId_actionPerformed(ActionEvent e)
2639 public void pdbFile_actionPerformed(ActionEvent e)
2644 public void invertColSel_actionPerformed(ActionEvent e)
2649 public void tabSelectionChanged(int sel)
2654 public void tabbedPane_mousePressed(MouseEvent e)
2659 public void tabbedPane_focusGained(FocusEvent e)
2664 public void save_actionPerformed(ActionEvent e)
2669 public void reload_actionPerformed(ActionEvent e)
2674 public void newView_actionPerformed(ActionEvent e)
2679 public void textColour_actionPerformed()
2684 public void idRightAlign_actionPerformed(ActionEvent e)
2689 public void expandViews_actionPerformed(ActionEvent e)
2694 public void gatherViews_actionPerformed(ActionEvent e)
2699 public void buildTreeSortMenu()
2704 public void pageSetup_actionPerformed(ActionEvent e)
2709 public void alignmentProperties()
2714 protected void expand_newalign(ActionEvent e)
2716 // TODO Auto-generated method stub
2720 protected boolean isShowAutoCalculatedAbove()
2722 return showAutoCalculatedAbove;
2725 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2727 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2730 protected SequenceAnnotationOrder getAnnotationSortOrder()
2732 return annotationSortOrder;
2735 protected void setAnnotationSortOrder(
2736 SequenceAnnotationOrder annotationSortOrder)
2738 this.annotationSortOrder = annotationSortOrder;
2741 public Map<KeyStroke, JMenuItem> getAccelerators()
2743 return this.accelerators;
2747 * Returns the selected index of the tabbed pane, or -1 if none selected
2748 * (including the case where the tabbed pane has not been made visible).
2752 public int getTabIndex()
2754 return tabbedPane.getSelectedIndex();
2757 public JPanel getStatusPanel()
2763 * Sets a reference to the containing split frame. Also makes the 'toggle
2764 * split view' menu item visible and checked.
2768 public void setSplitFrame(SplitContainerI sf)
2770 this.splitFrame = sf;
2773 this.showComplementMenuItem.setVisible(true);
2774 this.showComplementMenuItem.setState(true);
2778 public SplitContainerI getSplitViewContainer()
2780 return this.splitFrame;
2783 protected void showComplement_actionPerformed(boolean complement)
2787 protected void showInformationHistogram_actionPerformed(ActionEvent e)
2789 // TODO Auto-generated method stub
2793 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2795 // TODO Auto-generated method stub
2799 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2801 // TODO Auto-generated method stub