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 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
308 MessageManager.getString("action.select_all"));
309 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
310 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
311 al = new ActionListener()
314 public void actionPerformed(ActionEvent e)
316 selectAllSequenceMenuItem_actionPerformed(e);
319 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
321 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
322 MessageManager.getString("action.deselect_all"));
323 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
324 al = new ActionListener()
327 public void actionPerformed(ActionEvent e)
329 deselectAllSequenceMenuItem_actionPerformed(e);
332 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
334 JMenuItem invertSequenceMenuItem = new JMenuItem(
335 MessageManager.getString("action.invert_sequence_selection"));
336 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
337 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
338 al = new ActionListener()
341 public void actionPerformed(ActionEvent e)
343 invertSequenceMenuItem_actionPerformed(e);
346 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
348 JMenuItem grpsFromSelection = new JMenuItem(
349 MessageManager.getString("action.make_groups_selection"));
350 grpsFromSelection.addActionListener(new ActionListener()
353 public void actionPerformed(ActionEvent e)
355 makeGrpsFromSelection_actionPerformed(e);
358 JMenuItem expandAlignment = new JMenuItem(
359 MessageManager.getString("action.view_flanking_regions"));
360 expandAlignment.setToolTipText(MessageManager
361 .getString("label.view_flanking_regions"));
362 expandAlignment.addActionListener(new ActionListener()
365 public void actionPerformed(ActionEvent e)
370 JMenuItem remove2LeftMenuItem = new JMenuItem(
371 MessageManager.getString("action.remove_left"));
372 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
373 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
374 al = new ActionListener()
377 public void actionPerformed(ActionEvent e)
379 remove2LeftMenuItem_actionPerformed(e);
382 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
384 JMenuItem remove2RightMenuItem = new JMenuItem(
385 MessageManager.getString("action.remove_right"));
386 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
387 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
388 al = new ActionListener()
391 public void actionPerformed(ActionEvent e)
393 remove2RightMenuItem_actionPerformed(e);
396 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
398 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
399 MessageManager.getString("action.remove_empty_columns"));
400 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
401 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
402 al = new ActionListener()
405 public void actionPerformed(ActionEvent e)
407 removeGappedColumnMenuItem_actionPerformed(e);
410 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
412 JMenuItem removeAllGapsMenuItem = new JMenuItem(
413 MessageManager.getString("action.remove_all_gaps"));
414 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
415 .getDefaultToolkit().getMenuShortcutKeyMask()
416 | KeyEvent.SHIFT_MASK, false);
417 al = new ActionListener()
420 public void actionPerformed(ActionEvent e)
422 removeAllGapsMenuItem_actionPerformed(e);
425 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
427 JMenuItem justifyLeftMenuItem = new JMenuItem(
428 MessageManager.getString("action.left_justify_alignment"));
429 justifyLeftMenuItem.addActionListener(new ActionListener()
432 public void actionPerformed(ActionEvent e)
434 justifyLeftMenuItem_actionPerformed(e);
437 JMenuItem justifyRightMenuItem = new JMenuItem(
438 MessageManager.getString("action.right_justify_alignment"));
439 justifyRightMenuItem.addActionListener(new ActionListener()
442 public void actionPerformed(ActionEvent e)
444 justifyRightMenuItem_actionPerformed(e);
447 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
448 viewBoxesMenuItem.setState(true);
449 viewBoxesMenuItem.addActionListener(new ActionListener()
452 public void actionPerformed(ActionEvent e)
454 viewBoxesMenuItem_actionPerformed(e);
457 viewTextMenuItem.setText(MessageManager.getString("action.text"));
458 viewTextMenuItem.setState(true);
459 viewTextMenuItem.addActionListener(new ActionListener()
462 public void actionPerformed(ActionEvent e)
464 viewTextMenuItem_actionPerformed(e);
467 showNonconservedMenuItem.setText(MessageManager
468 .getString("label.show_non_conserved"));
469 showNonconservedMenuItem.setState(false);
470 showNonconservedMenuItem.addActionListener(new ActionListener()
473 public void actionPerformed(ActionEvent e)
475 showUnconservedMenuItem_actionPerformed(e);
478 JMenuItem sortPairwiseMenuItem = new JMenuItem(
479 MessageManager.getString("action.by_pairwise_id"));
480 sortPairwiseMenuItem.addActionListener(new ActionListener()
483 public void actionPerformed(ActionEvent e)
485 sortPairwiseMenuItem_actionPerformed(e);
488 JMenuItem sortIDMenuItem = new JMenuItem(
489 MessageManager.getString("action.by_id"));
490 sortIDMenuItem.addActionListener(new ActionListener()
493 public void actionPerformed(ActionEvent e)
495 sortIDMenuItem_actionPerformed(e);
498 JMenuItem sortLengthMenuItem = new JMenuItem(
499 MessageManager.getString("action.by_length"));
500 sortLengthMenuItem.addActionListener(new ActionListener()
503 public void actionPerformed(ActionEvent e)
505 sortLengthMenuItem_actionPerformed(e);
508 JMenuItem sortGroupMenuItem = new JMenuItem(
509 MessageManager.getString("action.by_group"));
510 sortGroupMenuItem.addActionListener(new ActionListener()
513 public void actionPerformed(ActionEvent e)
515 sortGroupMenuItem_actionPerformed(e);
519 JMenuItem removeRedundancyMenuItem = new JMenuItem(
520 MessageManager.getString("action.remove_redundancy"));
521 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
522 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
523 al = new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 removeRedundancyMenuItem_actionPerformed(e);
531 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
533 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
534 MessageManager.getString("action.pairwise_alignment"));
535 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
538 public void actionPerformed(ActionEvent e)
540 pairwiseAlignmentMenuItem_actionPerformed(e);
544 this.getContentPane().setLayout(new BorderLayout());
545 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
546 statusBar.setBackground(Color.white);
547 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
548 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
549 statusBar.setText(MessageManager.getString("label.status_bar"));
550 outputTextboxMenu.setText(MessageManager
551 .getString("label.out_to_textbox"));
553 annotationPanelMenuItem.setActionCommand("");
554 annotationPanelMenuItem.setText(MessageManager
555 .getString("label.show_annotations"));
556 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
558 annotationPanelMenuItem.addActionListener(new ActionListener()
561 public void actionPerformed(ActionEvent e)
563 annotationPanelMenuItem_actionPerformed(e);
566 showAllAlAnnotations.setText(MessageManager
567 .getString("label.show_all_al_annotations"));
568 final boolean isAnnotationPanelShown = annotationPanelMenuItem
570 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
571 showAllAlAnnotations.addActionListener(new ActionListener()
574 public void actionPerformed(ActionEvent e)
576 showAllAnnotations_actionPerformed(false, true);
579 hideAllAlAnnotations.setText(MessageManager
580 .getString("label.hide_all_al_annotations"));
581 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
582 hideAllAlAnnotations.addActionListener(new ActionListener()
585 public void actionPerformed(ActionEvent e)
587 hideAllAnnotations_actionPerformed(false, true);
590 showAllSeqAnnotations.setText(MessageManager
591 .getString("label.show_all_seq_annotations"));
592 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
593 showAllSeqAnnotations.addActionListener(new ActionListener()
596 public void actionPerformed(ActionEvent e)
598 showAllAnnotations_actionPerformed(true, false);
601 hideAllSeqAnnotations.setText(MessageManager
602 .getString("label.hide_all_seq_annotations"));
603 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
604 hideAllSeqAnnotations.addActionListener(new ActionListener()
607 public void actionPerformed(ActionEvent e)
609 hideAllAnnotations_actionPerformed(true, false);
612 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
613 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
614 SequenceAnnotationOrder.NONE.name()));
615 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
616 MessageManager.getString("label.sort_annotations_by_sequence"));
617 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
618 MessageManager.getString("label.sort_annotations_by_label"));
621 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
622 sortAnnBySequence.addActionListener(new ActionListener()
625 public void actionPerformed(ActionEvent e)
627 boolean newState = sortAnnBySequence.getState();
628 sortAnnByLabel.setSelected(false);
629 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
630 : SequenceAnnotationOrder.NONE);
631 sortAnnotations_actionPerformed();
635 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
636 sortAnnByLabel.addActionListener(new ActionListener()
639 public void actionPerformed(ActionEvent e)
641 boolean newState = sortAnnByLabel.getState();
642 sortAnnBySequence.setSelected(false);
643 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
644 : SequenceAnnotationOrder.NONE);
645 sortAnnotations_actionPerformed();
648 colourTextMenuItem = new JCheckBoxMenuItem(
650 .getString("label.colour_text"));
651 colourTextMenuItem.addActionListener(new ActionListener()
654 public void actionPerformed(ActionEvent e)
656 colourTextMenuItem_actionPerformed(e);
660 JMenuItem htmlMenuItem = new JMenuItem(
661 MessageManager.getString("label.html"));
662 htmlMenuItem.addActionListener(new ActionListener()
665 public void actionPerformed(ActionEvent e)
667 htmlMenuItem_actionPerformed(e);
671 JMenuItem createBioJS = new JMenuItem(
672 MessageManager.getString("label.biojs_html_export"));
673 createBioJS.addActionListener(new java.awt.event.ActionListener()
676 public void actionPerformed(ActionEvent e)
678 bioJSMenuItem_actionPerformed(e);
682 JMenuItem overviewMenuItem = new JMenuItem(
683 MessageManager.getString("label.overview_window"));
684 overviewMenuItem.addActionListener(new ActionListener()
687 public void actionPerformed(ActionEvent e)
689 overviewMenuItem_actionPerformed(e);
693 undoMenuItem.setEnabled(false);
694 undoMenuItem.setText(MessageManager.getString("action.undo"));
695 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
696 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
697 al = new ActionListener()
700 public void actionPerformed(ActionEvent e)
702 undoMenuItem_actionPerformed(e);
705 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
707 redoMenuItem.setEnabled(false);
708 redoMenuItem.setText(MessageManager.getString("action.redo"));
709 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
710 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
711 al = new ActionListener()
714 public void actionPerformed(ActionEvent e)
716 redoMenuItem_actionPerformed(e);
719 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
721 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
722 wrapMenuItem.addActionListener(new ActionListener()
725 public void actionPerformed(ActionEvent e)
727 wrapMenuItem_actionPerformed(e);
731 JMenuItem printMenuItem = new JMenuItem(
732 MessageManager.getString("action.print"));
733 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
734 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
735 al = new ActionListener()
738 public void actionPerformed(ActionEvent e)
740 printMenuItem_actionPerformed(e);
743 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
746 .setText(MessageManager.getString("action.show_gaps"));
747 renderGapsMenuItem.setState(true);
748 renderGapsMenuItem.addActionListener(new ActionListener()
751 public void actionPerformed(ActionEvent e)
753 renderGapsMenuItem_actionPerformed(e);
757 JMenuItem findMenuItem = new JMenuItem(
758 MessageManager.getString("action.find"));
759 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
760 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
761 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
762 MessageManager.getString("label.find_tip")));
763 al = new ActionListener()
766 public void actionPerformed(ActionEvent e)
768 findMenuItem_actionPerformed(e);
771 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
773 showSeqFeatures.setText(MessageManager
774 .getString("label.show_sequence_features"));
775 showSeqFeatures.addActionListener(new ActionListener()
778 public void actionPerformed(ActionEvent actionEvent)
780 showSeqFeatures_actionPerformed(actionEvent);
784 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
785 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
786 * void actionPerformed(ActionEvent actionEvent) {
787 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
789 showDbRefsMenuitem.setText(MessageManager
790 .getString("label.show_database_refs"));
791 showDbRefsMenuitem.addActionListener(new ActionListener()
795 public void actionPerformed(ActionEvent e)
797 showDbRefs_actionPerformed(e);
801 showNpFeatsMenuitem.setText(MessageManager
802 .getString("label.show_non_positional_features"));
803 showNpFeatsMenuitem.addActionListener(new ActionListener()
807 public void actionPerformed(ActionEvent e)
809 showNpFeats_actionPerformed(e);
813 showGroupConservation.setText(MessageManager
814 .getString("label.group_conservation"));
815 showGroupConservation.addActionListener(new ActionListener()
819 public void actionPerformed(ActionEvent e)
821 showGroupConservation_actionPerformed(e);
826 showGroupConsensus.setText(MessageManager
827 .getString("label.group_consensus"));
828 showGroupConsensus.addActionListener(new ActionListener()
832 public void actionPerformed(ActionEvent e)
834 showGroupConsensus_actionPerformed(e);
838 showConsensusHistogram.setText(MessageManager
839 .getString("label.show_consensus_histogram"));
840 showConsensusHistogram.addActionListener(new ActionListener()
844 public void actionPerformed(ActionEvent e)
846 showConsensusHistogram_actionPerformed(e);
850 showSequenceLogo.setText(MessageManager
851 .getString("label.show_consensus_logo"));
852 showSequenceLogo.addActionListener(new ActionListener()
856 public void actionPerformed(ActionEvent e)
858 showSequenceLogo_actionPerformed(e);
862 normaliseSequenceLogo.setText(MessageManager
863 .getString("label.norm_consensus_logo"));
864 normaliseSequenceLogo.addActionListener(new ActionListener()
868 public void actionPerformed(ActionEvent e)
870 normaliseSequenceLogo_actionPerformed(e);
874 applyAutoAnnotationSettings.setText(MessageManager
875 .getString("label.apply_all_groups"));
876 applyAutoAnnotationSettings.setState(false);
877 applyAutoAnnotationSettings.setVisible(true);
878 applyAutoAnnotationSettings.addActionListener(new ActionListener()
881 public void actionPerformed(ActionEvent e)
883 applyAutoAnnotationSettings_actionPerformed(e);
887 ButtonGroup buttonGroup = new ButtonGroup();
888 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
889 MessageManager.getString("label.show_first"));
890 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
891 MessageManager.getString("label.show_last"));
892 buttonGroup.add(showAutoFirst);
893 buttonGroup.add(showAutoLast);
894 final boolean autoFirst = Cache.getDefault(
895 Preferences.SHOW_AUTOCALC_ABOVE, false);
896 showAutoFirst.setSelected(autoFirst);
897 setShowAutoCalculatedAbove(autoFirst);
898 showAutoFirst.addActionListener(new ActionListener()
901 public void actionPerformed(ActionEvent e)
903 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
904 sortAnnotations_actionPerformed();
907 showAutoLast.setSelected(!showAutoFirst.isSelected());
908 showAutoLast.addActionListener(new ActionListener()
911 public void actionPerformed(ActionEvent e)
913 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
914 sortAnnotations_actionPerformed();
918 JMenuItem deleteGroups = new JMenuItem(
919 MessageManager.getString("action.undefine_groups"));
920 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
921 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
922 al = new ActionListener()
925 public void actionPerformed(ActionEvent e)
927 deleteGroups_actionPerformed(e);
930 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
932 JMenuItem annotationColumn = new JMenuItem(
933 MessageManager.getString("action.select_by_annotation"));
934 annotationColumn.addActionListener(new ActionListener()
937 public void actionPerformed(ActionEvent e)
939 annotationColumn_actionPerformed(e);
943 JMenuItem createGroup = new JMenuItem(
944 MessageManager.getString("action.create_group"));
945 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
946 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
947 al = new ActionListener()
950 public void actionPerformed(ActionEvent e)
952 createGroup_actionPerformed(e);
955 addMenuActionAndAccelerator(keyStroke, createGroup, al);
957 JMenuItem unGroup = new JMenuItem(
958 MessageManager.getString("action.remove_group"));
959 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
960 .getDefaultToolkit().getMenuShortcutKeyMask()
961 | KeyEvent.SHIFT_MASK, false);
962 al = new ActionListener()
965 public void actionPerformed(ActionEvent e)
967 unGroup_actionPerformed(e);
970 addMenuActionAndAccelerator(keyStroke, unGroup, al);
972 copy.setText(MessageManager.getString("action.copy"));
973 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
974 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
976 al = new ActionListener()
979 public void actionPerformed(ActionEvent e)
981 copy_actionPerformed(e);
984 addMenuActionAndAccelerator(keyStroke, copy, al);
986 cut.setText(MessageManager.getString("action.cut"));
987 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
988 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
989 al = new ActionListener()
992 public void actionPerformed(ActionEvent e)
994 cut_actionPerformed(e);
997 addMenuActionAndAccelerator(keyStroke, cut, al);
999 JMenuItem delete = new JMenuItem(
1000 MessageManager.getString("action.delete"));
1001 delete.addActionListener(new ActionListener()
1004 public void actionPerformed(ActionEvent e)
1006 delete_actionPerformed(e);
1010 pasteMenu.setText(MessageManager.getString("action.paste"));
1011 JMenuItem pasteNew = new JMenuItem(
1012 MessageManager.getString("label.to_new_alignment"));
1013 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1014 .getDefaultToolkit().getMenuShortcutKeyMask()
1015 | KeyEvent.SHIFT_MASK, false);
1016 al = new ActionListener()
1019 public void actionPerformed(ActionEvent e)
1023 pasteNew_actionPerformed(e);
1024 } catch (IOException | InterruptedException e1)
1026 // TODO Auto-generated catch block
1027 e1.printStackTrace();
1031 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1033 JMenuItem pasteThis = new JMenuItem(
1034 MessageManager.getString("label.to_this_alignment"));
1035 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1036 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1037 al = new ActionListener()
1040 public void actionPerformed(ActionEvent e)
1044 pasteThis_actionPerformed(e);
1045 } catch (IOException | InterruptedException e1)
1047 // TODO Auto-generated catch block
1048 e1.printStackTrace();
1052 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1054 JMenuItem createPNG = new JMenuItem("PNG");
1055 createPNG.addActionListener(new ActionListener()
1058 public void actionPerformed(ActionEvent e)
1063 createPNG.setActionCommand(MessageManager
1064 .getString("label.save_png_image"));
1066 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1067 font.addActionListener(new ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 font_actionPerformed(e);
1075 seqLimits.setText(MessageManager
1076 .getString("label.show_sequence_limits"));
1077 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1078 seqLimits.addActionListener(new ActionListener()
1081 public void actionPerformed(ActionEvent e)
1083 seqLimit_actionPerformed(e);
1086 JMenuItem epsFile = new JMenuItem("EPS");
1087 epsFile.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1096 JMenuItem createSVG = new JMenuItem("SVG");
1097 createSVG.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1106 JMenuItem loadTreeMenuItem = new JMenuItem(
1107 MessageManager.getString("label.load_associated_tree"));
1108 loadTreeMenuItem.setActionCommand(MessageManager
1109 .getString("label.load_tree_for_sequence_set"));
1110 loadTreeMenuItem.addActionListener(new ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 loadTreeMenuItem_actionPerformed(e);
1119 scaleAbove.setVisible(false);
1120 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1121 scaleAbove.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 scaleAbove_actionPerformed(e);
1129 scaleLeft.setVisible(false);
1130 scaleLeft.setSelected(true);
1131 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1132 scaleLeft.addActionListener(new ActionListener()
1135 public void actionPerformed(ActionEvent e)
1137 scaleLeft_actionPerformed(e);
1140 scaleRight.setVisible(false);
1141 scaleRight.setSelected(true);
1142 scaleRight.setText(MessageManager.getString("action.scale_right"));
1143 scaleRight.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 scaleRight_actionPerformed(e);
1151 centreColumnLabelsMenuItem.setVisible(true);
1152 centreColumnLabelsMenuItem.setState(false);
1153 centreColumnLabelsMenuItem.setText(MessageManager
1154 .getString("label.centre_column_labels"));
1155 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1158 public void actionPerformed(ActionEvent e)
1160 centreColumnLabels_actionPerformed(e);
1163 followHighlightMenuItem.setVisible(true);
1164 followHighlightMenuItem.setState(true);
1165 followHighlightMenuItem.setText(MessageManager
1166 .getString("label.automatic_scrolling"));
1167 followHighlightMenuItem.addActionListener(new ActionListener()
1171 public void actionPerformed(ActionEvent e)
1173 followHighlight_actionPerformed();
1179 .setText(MessageManager.getString("action.by_tree_order"));
1180 sort.setText(MessageManager.getString("action.sort"));
1181 sort.addMenuListener(new MenuListener()
1184 public void menuSelected(MenuEvent e)
1186 buildTreeSortMenu();
1190 public void menuDeselected(MenuEvent e)
1195 public void menuCanceled(MenuEvent e)
1199 sortByAnnotScore.setText(MessageManager
1200 .getString("label.sort_by_score"));
1201 sort.add(sortByAnnotScore);
1202 sort.addMenuListener(new javax.swing.event.MenuListener()
1206 public void menuCanceled(MenuEvent e)
1211 public void menuDeselected(MenuEvent e)
1216 public void menuSelected(MenuEvent e)
1218 buildSortByAnnotationScoresMenu();
1221 sortByAnnotScore.setVisible(false);
1223 calculateTree.setText(MessageManager
1224 .getString("action.calculate_tree_pca"));
1226 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1227 padGapsMenuitem.setState(jalview.bin.Cache
1228 .getDefault("PAD_GAPS", false));
1229 padGapsMenuitem.addActionListener(new ActionListener()
1232 public void actionPerformed(ActionEvent e)
1234 padGapsMenuitem_actionPerformed(e);
1237 JMenuItem vamsasStore = new JMenuItem(
1238 MessageManager.getString("label.vamsas_store"));
1239 vamsasStore.setVisible(false);
1240 vamsasStore.addActionListener(new ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 vamsasStore_actionPerformed(e);
1248 showTranslation.setText(MessageManager
1249 .getString("label.translate_cDNA"));
1250 showTranslation.addActionListener(new ActionListener()
1253 public void actionPerformed(ActionEvent e)
1255 showTranslation_actionPerformed(e);
1258 showReverse.setText(MessageManager.getString("label.reverse"));
1259 showReverse.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 showReverse_actionPerformed(false);
1267 showReverseComplement.setText(MessageManager
1268 .getString("label.reverse_complement"));
1269 showReverseComplement.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 showReverse_actionPerformed(true);
1278 JMenuItem extractScores = new JMenuItem(
1279 MessageManager.getString("label.extract_scores"));
1280 extractScores.addActionListener(new ActionListener()
1283 public void actionPerformed(ActionEvent e)
1285 extractScores_actionPerformed(e);
1288 extractScores.setVisible(true);
1289 // JBPNote: TODO: make gui for regex based score extraction
1291 // for show products actions see AlignFrame.canShowProducts
1292 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1294 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1295 runGroovy.setToolTipText(MessageManager
1296 .getString("label.run_groovy_tip"));
1297 runGroovy.addActionListener(new ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 runGroovy_actionPerformed();
1306 JMenuItem openFeatureSettings = new JMenuItem(
1307 MessageManager.getString("action.feature_settings"));
1308 openFeatureSettings.addActionListener(new ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 featureSettings_actionPerformed(e);
1316 JMenuItem fetchSequence = new JMenuItem(
1317 MessageManager.getString("label.fetch_sequences"));
1318 fetchSequence.addActionListener(new ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 fetchSequence_actionPerformed(e);
1327 JMenuItem associatedData = new JMenuItem(
1328 MessageManager.getString("label.load_features_annotations"));
1329 associatedData.addActionListener(new ActionListener()
1332 public void actionPerformed(ActionEvent e)
1336 associatedData_actionPerformed(e);
1337 } catch (IOException | InterruptedException e1)
1339 // TODO Auto-generated catch block
1340 e1.printStackTrace();
1344 autoCalculate.setText(MessageManager
1345 .getString("label.autocalculate_consensus"));
1346 autoCalculate.setState(jalview.bin.Cache.getDefault(
1347 "AUTO_CALC_CONSENSUS", true));
1348 autoCalculate.addActionListener(new ActionListener()
1351 public void actionPerformed(ActionEvent e)
1353 autoCalculate_actionPerformed(e);
1356 sortByTree.setText(MessageManager
1357 .getString("label.sort_alignment_new_tree"));
1359 .setToolTipText("<html>"
1361 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1363 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1364 sortByTree.addActionListener(new ActionListener()
1367 public void actionPerformed(ActionEvent e)
1369 sortByTreeOption_actionPerformed(e);
1373 listenToViewSelections.setText(MessageManager
1374 .getString("label.listen_for_selections"));
1375 listenToViewSelections
1376 .setToolTipText("<html>"
1378 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1379 listenToViewSelections.setState(false);
1380 listenToViewSelections.addActionListener(new ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 listenToViewSelections_actionPerformed(e);
1389 JMenu addSequenceMenu = new JMenu(
1390 MessageManager.getString("label.add_sequences"));
1391 JMenuItem addFromFile = new JMenuItem(
1392 MessageManager.getString("label.from_file"));
1393 addFromFile.addActionListener(new ActionListener()
1396 public void actionPerformed(ActionEvent e)
1398 addFromFile_actionPerformed(e);
1401 JMenuItem addFromText = new JMenuItem(
1402 MessageManager.getString("label.from_textbox"));
1403 addFromText.addActionListener(new ActionListener()
1406 public void actionPerformed(ActionEvent e)
1408 addFromText_actionPerformed(e);
1411 JMenuItem addFromURL = new JMenuItem(
1412 MessageManager.getString("label.from_url"));
1413 addFromURL.addActionListener(new ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 addFromURL_actionPerformed(e);
1421 JMenuItem exportFeatures = new JMenuItem(
1422 MessageManager.getString("label.export_features"));
1423 exportFeatures.addActionListener(new ActionListener()
1426 public void actionPerformed(ActionEvent e)
1428 exportFeatures_actionPerformed(e);
1431 JMenuItem exportAnnotations = new JMenuItem(
1432 MessageManager.getString("label.export_annotations"));
1433 exportAnnotations.addActionListener(new ActionListener()
1436 public void actionPerformed(ActionEvent e)
1438 exportAnnotations_actionPerformed(e);
1441 statusPanel.setLayout(new GridLayout());
1442 JMenuItem showAllSeqs = new JMenuItem(
1443 MessageManager.getString("label.all_sequences"));
1444 showAllSeqs.setToolTipText(MessageManager
1445 .getString("label.toggle_sequence_visibility"));
1446 showAllSeqs.addActionListener(new ActionListener()
1449 public void actionPerformed(ActionEvent e)
1451 showAllSeqs_actionPerformed(e);
1454 JMenuItem showAllColumns = new JMenuItem(
1455 MessageManager.getString("label.all_columns"));
1456 showAllColumns.setToolTipText(MessageManager
1457 .getString("label.toggle_columns_visibility"));
1458 showAllColumns.addActionListener(new ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 showAllColumns_actionPerformed(e);
1466 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1467 JMenuItem hideSelSequences = new JMenuItem(
1468 MessageManager.getString("label.selected_sequences"));
1469 hideSelSequences.setToolTipText(MessageManager
1470 .getString("label.toggle_sequence_visibility"));
1471 hideSelSequences.addActionListener(new ActionListener()
1474 public void actionPerformed(ActionEvent e)
1476 hideSelSequences_actionPerformed(e);
1479 JMenuItem hideSelColumns = new JMenuItem(
1480 MessageManager.getString("label.selected_columns"));
1481 hideSelColumns.setToolTipText(MessageManager
1482 .getString("label.toggle_columns_visibility"));
1483 hideSelColumns.addActionListener(new ActionListener()
1486 public void actionPerformed(ActionEvent e)
1488 hideSelColumns_actionPerformed(e);
1491 JMenuItem hideAllSelection = new JMenuItem(
1492 MessageManager.getString("label.selected_region"));
1493 hideAllSelection.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 hideAllSelection_actionPerformed(e);
1501 // TODO: should be hidden if no selection exists.
1502 JMenuItem hideAllButSelection = new JMenuItem(
1503 MessageManager.getString("label.all_but_selected_region"));
1504 hideAllButSelection.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 hideAllButSelection_actionPerformed(e);
1512 JMenuItem showAllhidden = new JMenuItem(
1513 MessageManager.getString("label.all_sequences_columns"));
1514 showAllhidden.setToolTipText(MessageManager
1515 .getString("label.toggles_visibility_hidden_selected_regions"));
1516 showAllhidden.addActionListener(new ActionListener()
1519 public void actionPerformed(ActionEvent e)
1521 showAllhidden_actionPerformed(e);
1524 hiddenMarkers.setText(MessageManager
1525 .getString("action.show_hidden_markers"));
1526 hiddenMarkers.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 hiddenMarkers_actionPerformed(e);
1535 JMenuItem invertColSel = new JMenuItem(
1536 MessageManager.getString("action.invert_column_selection"));
1537 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1538 .getDefaultToolkit().getMenuShortcutKeyMask()
1539 | KeyEvent.ALT_MASK, false);
1540 al = new ActionListener()
1543 public void actionPerformed(ActionEvent e)
1545 invertColSel_actionPerformed(e);
1548 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1550 showComplementMenuItem.setVisible(false);
1551 showComplementMenuItem.addActionListener(new ActionListener()
1554 public void actionPerformed(ActionEvent e)
1556 showComplement_actionPerformed(showComplementMenuItem.getState());
1560 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1563 public void stateChanged(ChangeEvent evt)
1565 JTabbedPane pane = (JTabbedPane) evt.getSource();
1566 int sel = pane.getSelectedIndex();
1567 tabSelectionChanged(sel);
1570 tabbedPane.addMouseListener(new MouseAdapter()
1573 public void mousePressed(MouseEvent e)
1575 if (e.isPopupTrigger()) // Mac
1577 tabbedPane_mousePressed(e);
1582 public void mouseReleased(MouseEvent e)
1584 if (e.isPopupTrigger()) // Windows
1586 tabbedPane_mousePressed(e);
1590 tabbedPane.addFocusListener(new FocusAdapter()
1593 public void focusGained(FocusEvent e)
1595 tabbedPane_focusGained(e);
1599 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1600 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
1601 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1602 al = new ActionListener()
1605 public void actionPerformed(ActionEvent e)
1607 save_actionPerformed(e);
1610 addMenuActionAndAccelerator(keyStroke, save, al);
1612 reload.setEnabled(false);
1613 reload.setText(MessageManager.getString("action.reload"));
1614 reload.addActionListener(new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 reload_actionPerformed(e);
1623 JMenuItem newView = new JMenuItem(
1624 MessageManager.getString("action.new_view"));
1625 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
1626 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1627 al = new ActionListener()
1630 public void actionPerformed(ActionEvent e)
1632 newView_actionPerformed(e);
1635 addMenuActionAndAccelerator(keyStroke, newView, al);
1637 tabbedPane.setToolTipText("<html><i>"
1638 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1641 formatMenu.setText(MessageManager.getString("action.format"));
1642 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1644 idRightAlign.setText(MessageManager
1645 .getString("label.right_align_sequence_id"));
1646 idRightAlign.addActionListener(new ActionListener()
1649 public void actionPerformed(ActionEvent e)
1651 idRightAlign_actionPerformed(e);
1655 gatherViews.setEnabled(false);
1656 gatherViews.setText(MessageManager.getString("action.gather_views"));
1657 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1658 al = new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 gatherViews_actionPerformed(e);
1666 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1668 expandViews.setEnabled(false);
1669 expandViews.setText(MessageManager.getString("action.expand_views"));
1670 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1671 al = new ActionListener()
1674 public void actionPerformed(ActionEvent e)
1676 expandViews_actionPerformed(e);
1679 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1681 JMenuItem pageSetup = new JMenuItem(
1682 MessageManager.getString("action.page_setup"));
1683 pageSetup.addActionListener(new ActionListener()
1686 public void actionPerformed(ActionEvent e)
1688 pageSetup_actionPerformed(e);
1691 JMenuItem alignmentProperties = new JMenuItem(
1692 MessageManager.getString("label.alignment_props"));
1693 alignmentProperties.addActionListener(new ActionListener()
1696 public void actionPerformed(ActionEvent actionEvent)
1698 alignmentProperties();
1701 JMenuItem selectHighlighted = new JMenuItem(
1702 MessageManager.getString("action.select_highlighted_columns"));
1703 selectHighlighted.setToolTipText(MessageManager
1704 .getString("tooltip.select_highlighted_columns"));
1705 al = new ActionListener()
1708 public void actionPerformed(ActionEvent actionEvent)
1710 selectHighlightedColumns_actionPerformed(actionEvent);
1713 hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
1714 hmmBuild.addActionListener(new ActionListener()
1718 public void actionPerformed(ActionEvent e)
1722 hmmBuild_actionPerformed(e);
1723 } catch (IOException e1)
1725 // TODO Auto-generated catch block
1726 e1.printStackTrace();
1727 } catch (InterruptedException e1)
1729 // TODO Auto-generated catch block
1730 e1.printStackTrace();
1735 hmmAlign.setText(MessageManager.getString("label.hmmalign"));
1736 hmmAlign.addActionListener(new ActionListener()
1740 public void actionPerformed(ActionEvent e)
1744 hmmAlign_actionPerformed(e);
1745 } catch (IOException e1)
1747 // TODO Auto-generated catch block
1748 e1.printStackTrace();
1749 } catch (InterruptedException e1)
1751 // TODO Auto-generated catch block
1752 e1.printStackTrace();
1757 selectHighlighted.addActionListener(al);
1758 JMenu tooltipSettingsMenu = new JMenu(
1759 MessageManager.getString("label.sequence_id_tooltip"));
1760 JMenu autoAnnMenu = new JMenu(
1761 MessageManager.getString("label.autocalculated_annotation"));
1763 JMenu exportImageMenu = new JMenu(
1764 MessageManager.getString("label.export_image"));
1765 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1766 alignFrameMenuBar.add(fileMenu);
1767 alignFrameMenuBar.add(editMenu);
1768 alignFrameMenuBar.add(selectMenu);
1769 alignFrameMenuBar.add(viewMenu);
1770 alignFrameMenuBar.add(annotationsMenu);
1771 alignFrameMenuBar.add(formatMenu);
1772 alignFrameMenuBar.add(colourMenu);
1773 alignFrameMenuBar.add(calculateMenu);
1774 alignFrameMenuBar.add(webService);
1775 alignFrameMenuBar.add(hmmerMenu);
1777 fileMenu.add(fetchSequence);
1778 fileMenu.add(addSequenceMenu);
1779 fileMenu.add(reload);
1780 fileMenu.addSeparator();
1781 fileMenu.add(vamsasStore);
1783 fileMenu.add(saveAs);
1784 fileMenu.add(outputTextboxMenu);
1785 fileMenu.add(pageSetup);
1786 fileMenu.add(printMenuItem);
1787 fileMenu.addSeparator();
1788 fileMenu.add(exportImageMenu);
1789 fileMenu.add(exportFeatures);
1790 fileMenu.add(exportAnnotations);
1791 fileMenu.add(loadTreeMenuItem);
1792 fileMenu.add(associatedData);
1793 fileMenu.addSeparator();
1794 fileMenu.add(closeMenuItem);
1796 pasteMenu.add(pasteNew);
1797 pasteMenu.add(pasteThis);
1798 editMenu.add(undoMenuItem);
1799 editMenu.add(redoMenuItem);
1802 editMenu.add(pasteMenu);
1803 editMenu.add(delete);
1804 editMenu.addSeparator();
1805 editMenu.add(remove2LeftMenuItem);
1806 editMenu.add(remove2RightMenuItem);
1807 editMenu.add(removeGappedColumnMenuItem);
1808 editMenu.add(removeAllGapsMenuItem);
1809 editMenu.add(removeRedundancyMenuItem);
1810 editMenu.addSeparator();
1811 // dont add these yet in the CVS build - they cannot be undone!
1812 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1813 // editMenu.add(justifyLeftMenuItem);
1814 // editMenu.add(justifyRightMenuItem);
1815 // editMenu.addSeparator();
1816 editMenu.add(padGapsMenuitem);
1818 showMenu.add(showAllColumns);
1819 showMenu.add(showAllSeqs);
1820 showMenu.add(showAllhidden);
1821 hideMenu.add(hideSelColumns);
1822 hideMenu.add(hideSelSequences);
1823 hideMenu.add(hideAllSelection);
1824 hideMenu.add(hideAllButSelection);
1825 viewMenu.add(newView);
1826 viewMenu.add(expandViews);
1827 viewMenu.add(gatherViews);
1828 viewMenu.addSeparator();
1829 viewMenu.add(showMenu);
1830 viewMenu.add(hideMenu);
1831 viewMenu.add(showComplementMenuItem);
1832 viewMenu.addSeparator();
1833 viewMenu.add(followHighlightMenuItem);
1834 viewMenu.addSeparator();
1835 viewMenu.add(showSeqFeatures);
1836 // viewMenu.add(showSeqFeaturesHeight);
1837 viewMenu.add(openFeatureSettings);
1838 tooltipSettingsMenu.add(showDbRefsMenuitem);
1839 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1840 viewMenu.add(tooltipSettingsMenu);
1841 viewMenu.addSeparator();
1842 viewMenu.add(alignmentProperties);
1843 viewMenu.addSeparator();
1844 viewMenu.add(overviewMenuItem);
1846 annotationsMenu.add(annotationPanelMenuItem);
1847 annotationsMenu.addSeparator();
1848 annotationsMenu.add(showAllAlAnnotations);
1849 annotationsMenu.add(hideAllAlAnnotations);
1850 annotationsMenu.addSeparator();
1851 annotationsMenu.add(showAllSeqAnnotations);
1852 annotationsMenu.add(hideAllSeqAnnotations);
1853 annotationsMenu.add(sortAnnBySequence);
1854 annotationsMenu.add(sortAnnByLabel);
1855 annotationsMenu.addSeparator();
1856 autoAnnMenu.add(showAutoFirst);
1857 autoAnnMenu.add(showAutoLast);
1858 autoAnnMenu.addSeparator();
1859 autoAnnMenu.add(applyAutoAnnotationSettings);
1860 autoAnnMenu.add(showConsensusHistogram);
1861 autoAnnMenu.add(showSequenceLogo);
1862 autoAnnMenu.add(normaliseSequenceLogo);
1863 autoAnnMenu.addSeparator();
1864 autoAnnMenu.add(showGroupConservation);
1865 autoAnnMenu.add(showGroupConsensus);
1866 annotationsMenu.add(autoAnnMenu);
1869 sort.add(sortIDMenuItem);
1870 sort.add(sortLengthMenuItem);
1871 sort.add(sortGroupMenuItem);
1872 sort.add(sortPairwiseMenuItem);
1873 sort.add(sortByTreeMenu);
1874 calculateMenu.add(sort);
1875 calculateMenu.add(calculateTree);
1876 calculateMenu.addSeparator();
1877 calculateMenu.add(pairwiseAlignmentMenuItem);
1878 calculateMenu.addSeparator();
1879 calculateMenu.add(showTranslation);
1880 calculateMenu.add(showReverse);
1881 calculateMenu.add(showReverseComplement);
1882 calculateMenu.add(showProducts);
1883 calculateMenu.add(autoCalculate);
1884 calculateMenu.add(sortByTree);
1885 calculateMenu.addSeparator();
1886 calculateMenu.add(expandAlignment);
1887 calculateMenu.add(extractScores);
1888 calculateMenu.addSeparator();
1889 calculateMenu.add(runGroovy);
1891 webServiceNoServices = new JMenuItem(
1892 MessageManager.getString("label.no_services"));
1893 webService.add(webServiceNoServices);
1894 exportImageMenu.add(htmlMenuItem);
1895 exportImageMenu.add(epsFile);
1896 exportImageMenu.add(createPNG);
1897 exportImageMenu.add(createBioJS);
1898 exportImageMenu.add(createSVG);
1899 addSequenceMenu.add(addFromFile);
1900 addSequenceMenu.add(addFromText);
1901 addSequenceMenu.add(addFromURL);
1902 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1903 statusPanel.add(statusBar, null);
1904 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1906 formatMenu.add(font);
1907 formatMenu.addSeparator();
1908 formatMenu.add(wrapMenuItem);
1909 formatMenu.add(scaleAbove);
1910 formatMenu.add(scaleLeft);
1911 formatMenu.add(scaleRight);
1912 formatMenu.add(seqLimits);
1913 formatMenu.add(idRightAlign);
1914 formatMenu.add(hiddenMarkers);
1915 formatMenu.add(viewBoxesMenuItem);
1916 formatMenu.add(viewTextMenuItem);
1917 formatMenu.add(colourTextMenuItem);
1918 formatMenu.add(renderGapsMenuItem);
1919 formatMenu.add(centreColumnLabelsMenuItem);
1920 formatMenu.add(showNonconservedMenuItem);
1921 selectMenu.add(findMenuItem);
1922 selectMenu.addSeparator();
1923 selectMenu.add(selectAllSequenceMenuItem);
1924 selectMenu.add(deselectAllSequenceMenuItem);
1925 selectMenu.add(invertSequenceMenuItem);
1926 selectMenu.add(invertColSel);
1927 selectMenu.add(createGroup);
1928 selectMenu.add(unGroup);
1929 selectMenu.add(grpsFromSelection);
1930 selectMenu.add(deleteGroups);
1931 selectMenu.add(annotationColumn);
1932 selectMenu.add(selectHighlighted);
1933 // TODO - determine if the listenToViewSelections button is needed : see bug
1935 // selectMenu.addSeparator();
1936 // selectMenu.add(listenToViewSelections);
1940 * Constructs the entries on the Colour menu (but does not add them to the
1943 protected void initHMMERMenu()
1945 hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
1946 hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
1947 hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
1949 protected void initColourMenu()
1951 applyToAllGroups = new JCheckBoxMenuItem(
1952 MessageManager.getString("label.apply_colour_to_all_groups"));
1953 applyToAllGroups.addActionListener(new ActionListener()
1956 public void actionPerformed(ActionEvent e)
1958 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
1962 textColour = new JMenuItem(
1963 MessageManager.getString("label.text_colour"));
1964 textColour.addActionListener(new ActionListener()
1967 public void actionPerformed(ActionEvent e)
1969 textColour_actionPerformed();
1973 conservationMenuItem = new JCheckBoxMenuItem(
1974 MessageManager.getString("action.by_conservation"));
1975 conservationMenuItem.addActionListener(new ActionListener()
1978 public void actionPerformed(ActionEvent e)
1980 conservationMenuItem_actionPerformed(conservationMenuItem
1985 abovePIDThreshold = new JCheckBoxMenuItem(
1986 MessageManager.getString("label.above_identity_threshold"));
1987 abovePIDThreshold.addActionListener(new ActionListener()
1990 public void actionPerformed(ActionEvent e)
1992 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
1995 modifyPID = new JMenuItem(
1996 MessageManager.getString("label.modify_identity_threshold"));
1997 modifyPID.addActionListener(new ActionListener()
2000 public void actionPerformed(ActionEvent e)
2002 modifyPID_actionPerformed();
2005 modifyConservation = new JMenuItem(
2007 .getString("label.modify_conservation_threshold"));
2008 modifyConservation.addActionListener(new ActionListener()
2011 public void actionPerformed(ActionEvent e)
2013 modifyConservation_actionPerformed();
2017 annotationColour = new JMenuItem(
2018 MessageManager.getString("action.by_annotation"));
2019 annotationColour.addActionListener(new ActionListener()
2022 public void actionPerformed(ActionEvent e)
2024 annotationColour_actionPerformed();
2029 protected void selectHighlightedColumns_actionPerformed(
2030 ActionEvent actionEvent)
2032 // TODO Auto-generated method stub
2037 * Generate the reverse sequence (or reverse complement if the flag is true)
2038 * and add it to the alignment
2042 protected void showReverse_actionPerformed(boolean complement)
2047 * Try to run script in a Groovy console, having first ensured that this
2048 * alignframe is set as currentAlignFrame in Desktop
2050 protected void runGroovy_actionPerformed()
2056 * Adds the given action listener and key accelerator to the given menu item.
2057 * Also saves in a lookup table to support lookup of action by key stroke.
2061 * @param actionListener
2063 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2064 JMenuItem menuItem, ActionListener actionListener)
2066 menuItem.setAccelerator(keyStroke);
2067 accelerators.put(keyStroke, menuItem);
2068 menuItem.addActionListener(actionListener);
2072 * Action on clicking sort annotations by type.
2076 protected void sortAnnotations_actionPerformed()
2081 * Action on clicking Show all annotations.
2083 * @param forSequences
2084 * update sequence-related annotations
2085 * @param forAlignment
2086 * update non-sequence-related annotations
2088 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2089 boolean forAlignment)
2091 setAnnotationsVisibility(true, forSequences, forAlignment);
2095 * Action on clicking Hide all annotations.
2097 * @param forSequences
2098 * update sequence-related annotations
2099 * @param forAlignment
2100 * update non-sequence-related annotations
2102 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2103 boolean forAlignment)
2105 setAnnotationsVisibility(false, forSequences, forAlignment);
2109 * Set the visibility of annotations to true or false. Can act on
2110 * sequence-related annotations, or alignment-related, or both.
2113 * @param forSequences
2114 * update sequence-related annotations
2115 * @param forAlignment
2116 * update non-sequence-related annotations
2118 protected void setAnnotationsVisibility(boolean visible,
2119 boolean forSequences, boolean forAlignment)
2124 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2126 // TODO Auto-generated method stub
2130 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2132 // TODO Auto-generated method stub
2136 protected void showAllhidden_actionPerformed(ActionEvent e)
2138 // TODO Auto-generated method stub
2142 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2144 // TODO Auto-generated method stub
2148 protected void hideAllSelection_actionPerformed(ActionEvent e)
2150 // TODO Auto-generated method stub
2154 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2156 // TODO Auto-generated method stub
2160 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2162 // TODO Auto-generated method stub
2166 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2168 // TODO Auto-generated method stub
2172 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2174 // TODO Auto-generated method stub
2178 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2180 // TODO Auto-generated method stub
2184 protected void showGroupConservation_actionPerformed(ActionEvent e)
2186 // TODO Auto-generated method stub
2190 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2192 // TODO Auto-generated method stub
2196 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2198 // TODO Auto-generated method stub
2202 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2204 // TODO Auto-generated method stub
2208 protected void followHighlight_actionPerformed()
2210 // TODO Auto-generated method stub
2214 protected void showNpFeats_actionPerformed(ActionEvent e)
2216 // TODO Auto-generated method stub
2220 protected void showDbRefs_actionPerformed(ActionEvent e)
2222 // TODO Auto-generated method stub
2226 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2230 protected void buildSortByAnnotationScoresMenu()
2234 protected void extractScores_actionPerformed(ActionEvent e)
2238 protected void outputText_actionPerformed(ActionEvent e)
2242 public void addFromFile_actionPerformed(ActionEvent e)
2247 public void addFromText_actionPerformed(ActionEvent e)
2252 public void addFromURL_actionPerformed(ActionEvent e)
2257 public void exportFeatures_actionPerformed(ActionEvent e)
2262 public void exportAnnotations_actionPerformed(ActionEvent e)
2267 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2271 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2276 protected void closeMenuItem_actionPerformed(boolean b)
2280 protected void redoMenuItem_actionPerformed(ActionEvent e)
2284 protected void undoMenuItem_actionPerformed(ActionEvent e)
2288 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2292 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2296 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2300 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2304 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2308 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2312 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2316 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2320 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2324 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2328 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2332 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2336 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2340 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2344 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2348 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2352 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2356 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2360 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2364 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2368 protected void conservationMenuItem_actionPerformed(boolean selected)
2372 protected void printMenuItem_actionPerformed(ActionEvent e)
2376 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2380 protected void findMenuItem_actionPerformed(ActionEvent e)
2384 protected void abovePIDThreshold_actionPerformed(boolean selected)
2388 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2392 protected void deleteGroups_actionPerformed(ActionEvent e)
2396 protected void createGroup_actionPerformed(ActionEvent e)
2400 protected void unGroup_actionPerformed(ActionEvent e)
2404 protected void copy_actionPerformed(ActionEvent e)
2408 protected void cut_actionPerformed(ActionEvent e)
2412 protected void delete_actionPerformed(ActionEvent e)
2416 protected void pasteNew_actionPerformed(ActionEvent e)
2417 throws IOException, InterruptedException
2421 protected void pasteThis_actionPerformed(ActionEvent e)
2422 throws IOException, InterruptedException
2426 protected void applyToAllGroups_actionPerformed(boolean selected)
2430 protected void autoAlignSeqs_actionPerformed(boolean selected)
2434 protected void hmmAlign_actionPerformed(ActionEvent e)
2435 throws IOException, InterruptedException
2439 protected void changeHMMERLocation_actionPerformed(ActionEvent e)
2443 protected void hmmBuild_actionPerformed(ActionEvent e)
2444 throws IOException, InterruptedException
2448 protected void hmmSearch_actionPerformed(ActionEvent e)
2452 public void createPNG(java.io.File f)
2456 protected void font_actionPerformed(ActionEvent e)
2460 protected void seqLimit_actionPerformed(ActionEvent e)
2464 public void seqDBRef_actionPerformed(ActionEvent e)
2469 public void createEPS(java.io.File f)
2473 public void createSVG(java.io.File f)
2478 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2484 * Template method to handle the 'load T-Coffee scores' menu event.
2486 * Subclasses override this method to provide a custom action.
2491 protected void loadScores_actionPerformed(ActionEvent event)
2496 protected void jpred_actionPerformed(ActionEvent e)
2500 protected void scaleAbove_actionPerformed(ActionEvent e)
2504 protected void scaleLeft_actionPerformed(ActionEvent e)
2508 protected void scaleRight_actionPerformed(ActionEvent e)
2512 protected void modifyPID_actionPerformed()
2516 protected void modifyConservation_actionPerformed()
2520 protected void saveAs_actionPerformed(ActionEvent e)
2524 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2528 public void vamsasStore_actionPerformed(ActionEvent e)
2533 public void vamsasLoad_actionPerformed(ActionEvent e)
2538 public void showTranslation_actionPerformed(ActionEvent e)
2543 public void featureSettings_actionPerformed(ActionEvent e)
2548 public void fetchSequence_actionPerformed(ActionEvent e)
2553 public void smoothFont_actionPerformed(ActionEvent e)
2558 public void annotationColour_actionPerformed()
2562 public void annotationColumn_actionPerformed(ActionEvent e)
2566 public void associatedData_actionPerformed(ActionEvent e)
2567 throws IOException, InterruptedException
2572 public void autoCalculate_actionPerformed(ActionEvent e)
2577 public void sortByTreeOption_actionPerformed(ActionEvent e)
2582 public void showAllSeqs_actionPerformed(ActionEvent e)
2587 public void showAllColumns_actionPerformed(ActionEvent e)
2592 public void hideSelSequences_actionPerformed(ActionEvent e)
2597 public void hideSelColumns_actionPerformed(ActionEvent e)
2602 public void hiddenMarkers_actionPerformed(ActionEvent e)
2607 public void findPdbId_actionPerformed(ActionEvent e)
2612 public void enterPdbId_actionPerformed(ActionEvent e)
2617 public void pdbFile_actionPerformed(ActionEvent e)
2622 public void invertColSel_actionPerformed(ActionEvent e)
2627 public void tabSelectionChanged(int sel)
2632 public void tabbedPane_mousePressed(MouseEvent e)
2637 public void tabbedPane_focusGained(FocusEvent e)
2642 public void save_actionPerformed(ActionEvent e)
2647 public void reload_actionPerformed(ActionEvent e)
2652 public void newView_actionPerformed(ActionEvent e)
2657 public void textColour_actionPerformed()
2662 public void idRightAlign_actionPerformed(ActionEvent e)
2667 public void expandViews_actionPerformed(ActionEvent e)
2672 public void gatherViews_actionPerformed(ActionEvent e)
2677 public void buildTreeSortMenu()
2682 public void pageSetup_actionPerformed(ActionEvent e)
2687 public void alignmentProperties()
2692 protected void expand_newalign(ActionEvent e)
2694 // TODO Auto-generated method stub
2698 protected boolean isShowAutoCalculatedAbove()
2700 return showAutoCalculatedAbove;
2703 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2705 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2708 protected SequenceAnnotationOrder getAnnotationSortOrder()
2710 return annotationSortOrder;
2713 protected void setAnnotationSortOrder(
2714 SequenceAnnotationOrder annotationSortOrder)
2716 this.annotationSortOrder = annotationSortOrder;
2719 public Map<KeyStroke, JMenuItem> getAccelerators()
2721 return this.accelerators;
2725 * Returns the selected index of the tabbed pane, or -1 if none selected
2726 * (including the case where the tabbed pane has not been made visible).
2730 public int getTabIndex()
2732 return tabbedPane.getSelectedIndex();
2735 public JPanel getStatusPanel()
2741 * Sets a reference to the containing split frame. Also makes the 'toggle
2742 * split view' menu item visible and checked.
2746 public void setSplitFrame(SplitContainerI sf)
2748 this.splitFrame = sf;
2751 this.showComplementMenuItem.setVisible(true);
2752 this.showComplementMenuItem.setState(true);
2756 public SplitContainerI getSplitViewContainer()
2758 return this.splitFrame;
2761 protected void showComplement_actionPerformed(boolean complement)
2765 protected void showInformationHistogram_actionPerformed(ActionEvent e)
2767 // TODO Auto-generated method stub
2771 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
2773 // TODO Auto-generated method stub
2777 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
2779 // TODO Auto-generated method stub