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.hmmer.HmmerCommand;
29 import jalview.io.FileFormatException;
30 import jalview.io.FileFormats;
31 import jalview.util.MessageManager;
32 import jalview.util.Platform;
34 import java.awt.BorderLayout;
35 import java.awt.Color;
36 import java.awt.GridLayout;
37 import java.awt.Toolkit;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.event.FocusAdapter;
41 import java.awt.event.FocusEvent;
42 import java.awt.event.KeyEvent;
43 import java.awt.event.MouseAdapter;
44 import java.awt.event.MouseEvent;
45 import java.io.IOException;
46 import java.util.HashMap;
49 import javax.swing.BorderFactory;
50 import javax.swing.ButtonGroup;
51 import javax.swing.JCheckBoxMenuItem;
52 import javax.swing.JInternalFrame;
53 import javax.swing.JLabel;
54 import javax.swing.JMenu;
55 import javax.swing.JMenuBar;
56 import javax.swing.JMenuItem;
57 import javax.swing.JPanel;
58 import javax.swing.JRadioButtonMenuItem;
59 import javax.swing.JTabbedPane;
60 import javax.swing.KeyStroke;
61 import javax.swing.event.ChangeEvent;
62 import javax.swing.event.MenuEvent;
63 import javax.swing.event.MenuListener;
65 public class GAlignFrame extends JInternalFrame
67 protected JMenuBar alignFrameMenuBar = new JMenuBar();
69 protected JMenuItem closeMenuItem = new JMenuItem();
71 protected JMenu webService = new JMenu();
73 protected JMenu hmmerMenu = new JMenu();
75 protected JMenuItem webServiceNoServices;
77 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
79 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
81 protected JMenu sortByAnnotScore = new JMenu();
83 public JLabel statusBar = new JLabel();
85 protected JMenu outputTextboxMenu = new JMenu();
87 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
89 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
91 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
93 protected JMenuItem undoMenuItem = new JMenuItem();
95 protected JMenuItem redoMenuItem = new JMenuItem();
97 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
99 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
101 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
103 JMenuItem copy = new JMenuItem();
105 JMenuItem cut = new JMenuItem();
107 JMenu pasteMenu = new JMenu();
109 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
111 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
113 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
115 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
117 protected JCheckBoxMenuItem applyToAllGroups;
119 protected JMenu colourMenu = new JMenu();
121 protected JMenuItem textColour;
123 protected JCheckBoxMenuItem conservationMenuItem;
125 protected JMenuItem modifyConservation;
127 protected JCheckBoxMenuItem abovePIDThreshold;
129 protected JMenuItem modifyPID;
131 protected JMenuItem annotationColour;
133 protected JMenu sortByTreeMenu = new JMenu();
135 protected JMenu sort = new JMenu();
137 protected JMenuItem calculateTree = new JMenuItem();
139 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
141 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
143 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
145 protected JMenuItem showTranslation = new JMenuItem();
147 protected JMenuItem showReverse = new JMenuItem();
149 protected JMenuItem showReverseComplement = new JMenuItem();
151 protected JMenu showProducts = new JMenu();
153 protected JMenuItem runGroovy = new JMenuItem();
155 protected JMenuItem loadVcf;
157 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
159 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
161 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
163 protected JPanel statusPanel = new JPanel();
165 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
167 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
169 protected JMenuItem showAllAlAnnotations = new JMenuItem();
171 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
173 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
175 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
177 protected JTabbedPane tabbedPane = new JTabbedPane();
179 protected JMenuItem reload = new JMenuItem();
181 protected JMenu formatMenu = new JMenu();
183 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
185 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
187 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
189 protected JMenuItem gatherViews = new JMenuItem();
191 protected JMenuItem expandViews = new JMenuItem();
193 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
197 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
199 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
201 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
203 protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
209 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
211 private SequenceAnnotationOrder annotationSortOrder;
213 private boolean showAutoCalculatedAbove = false;
215 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
217 private SplitContainerI splitFrame;
224 setJMenuBar(alignFrameMenuBar);
226 // dynamically fill save as menu with available formats
227 for (String ff : FileFormats.getInstance().getWritableFormats(true))
229 JMenuItem item = new JMenuItem(ff);
231 item.addActionListener(new ActionListener()
234 public void actionPerformed(ActionEvent e)
236 outputText_actionPerformed(e);
240 outputTextboxMenu.add(item);
242 } catch (Exception e)
244 System.err.println(e.toString());
247 if (!Platform.isAMac())
249 closeMenuItem.setMnemonic('C');
250 outputTextboxMenu.setMnemonic('T');
251 undoMenuItem.setMnemonic('Z');
252 redoMenuItem.setMnemonic('0');
253 copy.setMnemonic('C');
254 cut.setMnemonic('U');
255 pasteMenu.setMnemonic('P');
256 reload.setMnemonic('R');
260 private void jbInit() throws Exception
264 JMenuItem saveAs = new JMenuItem(
265 MessageManager.getString("action.save_as"));
266 ActionListener al = new ActionListener()
269 public void actionPerformed(ActionEvent e)
271 saveAs_actionPerformed(e);
275 // FIXME getDefaultToolkit throws an exception in Headless mode
276 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
277 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
278 | KeyEvent.SHIFT_MASK,
280 addMenuActionAndAccelerator(keyStroke, saveAs, al);
282 closeMenuItem.setText(MessageManager.getString("action.close"));
283 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
284 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
285 al = new ActionListener()
288 public void actionPerformed(ActionEvent e)
290 closeMenuItem_actionPerformed(false);
293 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
295 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
296 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
297 JMenu annotationsMenu = new JMenu(
298 MessageManager.getString("action.annotations"));
299 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
300 colourMenu.setText(MessageManager.getString("action.colour"));
301 JMenu calculateMenu = new JMenu(
302 MessageManager.getString("action.calculate"));
303 webService.setText(MessageManager.getString("action.web_service"));
307 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
308 MessageManager.getString("action.select_all"));
309 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
310 Toolkit.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,
337 Toolkit.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(
361 MessageManager.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,
373 Toolkit.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,
387 Toolkit.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,
401 Toolkit.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,
415 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
416 | KeyEvent.SHIFT_MASK,
418 al = new ActionListener()
421 public void actionPerformed(ActionEvent e)
423 removeAllGapsMenuItem_actionPerformed(e);
426 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
428 JMenuItem justifyLeftMenuItem = new JMenuItem(
429 MessageManager.getString("action.left_justify_alignment"));
430 justifyLeftMenuItem.addActionListener(new ActionListener()
433 public void actionPerformed(ActionEvent e)
435 justifyLeftMenuItem_actionPerformed(e);
438 JMenuItem justifyRightMenuItem = new JMenuItem(
439 MessageManager.getString("action.right_justify_alignment"));
440 justifyRightMenuItem.addActionListener(new ActionListener()
443 public void actionPerformed(ActionEvent e)
445 justifyRightMenuItem_actionPerformed(e);
448 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
449 viewBoxesMenuItem.setState(true);
450 viewBoxesMenuItem.addActionListener(new ActionListener()
453 public void actionPerformed(ActionEvent e)
455 viewBoxesMenuItem_actionPerformed(e);
458 viewTextMenuItem.setText(MessageManager.getString("action.text"));
459 viewTextMenuItem.setState(true);
460 viewTextMenuItem.addActionListener(new ActionListener()
463 public void actionPerformed(ActionEvent e)
465 viewTextMenuItem_actionPerformed(e);
468 showNonconservedMenuItem
469 .setText(MessageManager.getString("label.show_non_conserved"));
470 showNonconservedMenuItem.setState(false);
471 showNonconservedMenuItem.addActionListener(new ActionListener()
474 public void actionPerformed(ActionEvent e)
476 showUnconservedMenuItem_actionPerformed(e);
479 JMenuItem sortPairwiseMenuItem = new JMenuItem(
480 MessageManager.getString("action.by_pairwise_id"));
481 sortPairwiseMenuItem.addActionListener(new ActionListener()
484 public void actionPerformed(ActionEvent e)
486 sortPairwiseMenuItem_actionPerformed(e);
489 JMenuItem sortIDMenuItem = new JMenuItem(
490 MessageManager.getString("action.by_id"));
491 sortIDMenuItem.addActionListener(new ActionListener()
494 public void actionPerformed(ActionEvent e)
496 sortIDMenuItem_actionPerformed(e);
499 JMenuItem sortLengthMenuItem = new JMenuItem(
500 MessageManager.getString("action.by_length"));
501 sortLengthMenuItem.addActionListener(new ActionListener()
504 public void actionPerformed(ActionEvent e)
506 sortLengthMenuItem_actionPerformed(e);
509 JMenuItem sortGroupMenuItem = new JMenuItem(
510 MessageManager.getString("action.by_group"));
511 sortGroupMenuItem.addActionListener(new ActionListener()
514 public void actionPerformed(ActionEvent e)
516 sortGroupMenuItem_actionPerformed(e);
520 JMenuItem removeRedundancyMenuItem = new JMenuItem(
521 MessageManager.getString("action.remove_redundancy"));
522 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
523 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
524 al = new ActionListener()
527 public void actionPerformed(ActionEvent e)
529 removeRedundancyMenuItem_actionPerformed(e);
532 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
534 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
535 MessageManager.getString("action.pairwise_alignment"));
536 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
539 public void actionPerformed(ActionEvent e)
541 pairwiseAlignmentMenuItem_actionPerformed(e);
545 this.getContentPane().setLayout(new BorderLayout());
546 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
547 statusBar.setBackground(Color.white);
548 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
549 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
550 statusBar.setText(MessageManager.getString("label.status_bar"));
553 .setText(MessageManager.getString("label.out_to_textbox"));
556 annotationPanelMenuItem.setActionCommand("");
557 annotationPanelMenuItem
558 .setText(MessageManager.getString("label.show_annotations"));
559 annotationPanelMenuItem
560 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
561 annotationPanelMenuItem.addActionListener(new ActionListener()
564 public void actionPerformed(ActionEvent e)
566 annotationPanelMenuItem_actionPerformed(e);
569 showAllAlAnnotations.setText(
570 MessageManager.getString("label.show_all_al_annotations"));
571 final boolean isAnnotationPanelShown = annotationPanelMenuItem
573 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
574 showAllAlAnnotations.addActionListener(new ActionListener()
577 public void actionPerformed(ActionEvent e)
579 showAllAnnotations_actionPerformed(false, true);
582 hideAllAlAnnotations.setText(
583 MessageManager.getString("label.hide_all_al_annotations"));
584 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
585 hideAllAlAnnotations.addActionListener(new ActionListener()
588 public void actionPerformed(ActionEvent e)
590 hideAllAnnotations_actionPerformed(false, true);
593 showAllSeqAnnotations.setText(
594 MessageManager.getString("label.show_all_seq_annotations"));
595 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
596 showAllSeqAnnotations.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent e)
601 showAllAnnotations_actionPerformed(true, false);
604 hideAllSeqAnnotations.setText(
605 MessageManager.getString("label.hide_all_seq_annotations"));
606 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
607 hideAllSeqAnnotations.addActionListener(new ActionListener()
610 public void actionPerformed(ActionEvent e)
612 hideAllAnnotations_actionPerformed(true, false);
615 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
616 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
617 SequenceAnnotationOrder.NONE.name()));
618 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
619 MessageManager.getString("label.sort_annotations_by_sequence"));
620 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
621 MessageManager.getString("label.sort_annotations_by_label"));
624 sortAnnBySequence.setSelected(
625 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
626 sortAnnBySequence.addActionListener(new ActionListener()
629 public void actionPerformed(ActionEvent e)
631 boolean newState = sortAnnBySequence.getState();
632 sortAnnByLabel.setSelected(false);
633 setAnnotationSortOrder(
634 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
635 : SequenceAnnotationOrder.NONE);
636 sortAnnotations_actionPerformed();
639 sortAnnByLabel.setSelected(
640 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
641 sortAnnByLabel.addActionListener(new ActionListener()
644 public void actionPerformed(ActionEvent e)
646 boolean newState = sortAnnByLabel.getState();
647 sortAnnBySequence.setSelected(false);
648 setAnnotationSortOrder(
649 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
650 : SequenceAnnotationOrder.NONE);
651 sortAnnotations_actionPerformed();
654 colourTextMenuItem = new JCheckBoxMenuItem(
655 MessageManager.getString("label.colour_text"));
656 colourTextMenuItem.addActionListener(new ActionListener()
659 public void actionPerformed(ActionEvent e)
661 colourTextMenuItem_actionPerformed(e);
665 JMenuItem htmlMenuItem = new JMenuItem(
666 MessageManager.getString("label.html"));
667 htmlMenuItem.addActionListener(new ActionListener()
670 public void actionPerformed(ActionEvent e)
672 htmlMenuItem_actionPerformed(e);
676 JMenuItem createBioJS = new JMenuItem(
677 MessageManager.getString("label.biojs_html_export"));
678 createBioJS.addActionListener(new java.awt.event.ActionListener()
681 public void actionPerformed(ActionEvent e)
683 bioJSMenuItem_actionPerformed(e);
687 JMenuItem overviewMenuItem = new JMenuItem(
688 MessageManager.getString("label.overview_window"));
689 overviewMenuItem.addActionListener(new ActionListener()
692 public void actionPerformed(ActionEvent e)
694 overviewMenuItem_actionPerformed(e);
698 undoMenuItem.setEnabled(false);
699 undoMenuItem.setText(MessageManager.getString("action.undo"));
700 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
701 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
702 al = new ActionListener()
705 public void actionPerformed(ActionEvent e)
707 undoMenuItem_actionPerformed(e);
710 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
712 redoMenuItem.setEnabled(false);
713 redoMenuItem.setText(MessageManager.getString("action.redo"));
714 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
715 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
716 al = new ActionListener()
719 public void actionPerformed(ActionEvent e)
721 redoMenuItem_actionPerformed(e);
724 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
726 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
727 wrapMenuItem.addActionListener(new ActionListener()
730 public void actionPerformed(ActionEvent e)
732 wrapMenuItem_actionPerformed(e);
736 JMenuItem printMenuItem = new JMenuItem(
737 MessageManager.getString("action.print"));
738 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
739 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
740 al = new ActionListener()
743 public void actionPerformed(ActionEvent e)
745 printMenuItem_actionPerformed(e);
748 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
751 .setText(MessageManager.getString("action.show_gaps"));
752 renderGapsMenuItem.setState(true);
753 renderGapsMenuItem.addActionListener(new ActionListener()
756 public void actionPerformed(ActionEvent e)
758 renderGapsMenuItem_actionPerformed(e);
762 JMenuItem findMenuItem = new JMenuItem(
763 MessageManager.getString("action.find"));
764 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
765 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
766 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
767 MessageManager.getString("label.find_tip")));
768 al = new ActionListener()
771 public void actionPerformed(ActionEvent e)
773 findMenuItem_actionPerformed(e);
776 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
778 showSeqFeatures.setText(
779 MessageManager.getString("label.show_sequence_features"));
781 showSeqFeatures.addActionListener(new ActionListener()
784 public void actionPerformed(ActionEvent actionEvent)
786 showSeqFeatures_actionPerformed(actionEvent);
790 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
791 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
792 * void actionPerformed(ActionEvent actionEvent) {
793 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
796 .setText(MessageManager.getString("label.show_database_refs"));
797 showDbRefsMenuitem.addActionListener(new ActionListener()
801 public void actionPerformed(ActionEvent e)
803 showDbRefs_actionPerformed(e);
807 showNpFeatsMenuitem.setText(
808 MessageManager.getString("label.show_non_positional_features"));
809 showNpFeatsMenuitem.addActionListener(new ActionListener()
813 public void actionPerformed(ActionEvent e)
815 showNpFeats_actionPerformed(e);
819 showGroupConservation
820 .setText(MessageManager.getString("label.group_conservation"));
821 showGroupConservation.addActionListener(new ActionListener()
825 public void actionPerformed(ActionEvent e)
827 showGroupConservation_actionPerformed(e);
833 .setText(MessageManager.getString("label.group_consensus"));
834 showGroupConsensus.addActionListener(new ActionListener()
838 public void actionPerformed(ActionEvent e)
840 showGroupConsensus_actionPerformed(e);
844 showConsensusHistogram.setText(
845 MessageManager.getString("label.show_consensus_histogram"));
846 showConsensusHistogram.addActionListener(new ActionListener()
850 public void actionPerformed(ActionEvent e)
852 showConsensusHistogram_actionPerformed(e);
857 .setText(MessageManager.getString("label.show_consensus_logo"));
858 showSequenceLogo.addActionListener(new ActionListener()
862 public void actionPerformed(ActionEvent e)
864 showSequenceLogo_actionPerformed(e);
868 normaliseSequenceLogo
869 .setText(MessageManager.getString("label.norm_consensus_logo"));
870 normaliseSequenceLogo.addActionListener(new ActionListener()
874 public void actionPerformed(ActionEvent e)
876 normaliseSequenceLogo_actionPerformed(e);
880 applyAutoAnnotationSettings
881 .setText(MessageManager.getString("label.apply_all_groups"));
882 applyAutoAnnotationSettings.setState(false);
883 applyAutoAnnotationSettings.setVisible(true);
884 applyAutoAnnotationSettings.addActionListener(new ActionListener()
887 public void actionPerformed(ActionEvent e)
889 applyAutoAnnotationSettings_actionPerformed(e);
893 ButtonGroup buttonGroup = new ButtonGroup();
894 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
895 MessageManager.getString("label.show_first"));
896 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
897 MessageManager.getString("label.show_last"));
898 buttonGroup.add(showAutoFirst);
899 buttonGroup.add(showAutoLast);
900 final boolean autoFirst = Cache
901 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
902 showAutoFirst.setSelected(autoFirst);
903 setShowAutoCalculatedAbove(autoFirst);
904 showAutoFirst.addActionListener(new ActionListener()
907 public void actionPerformed(ActionEvent e)
909 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
910 sortAnnotations_actionPerformed();
913 showAutoLast.setSelected(!showAutoFirst.isSelected());
914 showAutoLast.addActionListener(new ActionListener()
917 public void actionPerformed(ActionEvent e)
919 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
920 sortAnnotations_actionPerformed();
924 JMenuItem deleteGroups = new JMenuItem(
925 MessageManager.getString("action.undefine_groups"));
926 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
927 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
928 al = new ActionListener()
931 public void actionPerformed(ActionEvent e)
933 deleteGroups_actionPerformed(e);
936 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
938 JMenuItem annotationColumn = new JMenuItem(
939 MessageManager.getString("action.select_by_annotation"));
940 annotationColumn.addActionListener(new ActionListener()
943 public void actionPerformed(ActionEvent e)
945 annotationColumn_actionPerformed(e);
949 JMenuItem createGroup = new JMenuItem(
950 MessageManager.getString("action.create_group"));
951 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
952 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
953 al = new ActionListener()
956 public void actionPerformed(ActionEvent e)
958 createGroup_actionPerformed(e);
961 addMenuActionAndAccelerator(keyStroke, createGroup, al);
963 JMenuItem unGroup = new JMenuItem(
964 MessageManager.getString("action.remove_group"));
965 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
966 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
967 | KeyEvent.SHIFT_MASK,
969 al = new ActionListener()
972 public void actionPerformed(ActionEvent e)
974 unGroup_actionPerformed(e);
977 addMenuActionAndAccelerator(keyStroke, unGroup, al);
979 copy.setText(MessageManager.getString("action.copy"));
980 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
981 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
983 al = new ActionListener()
986 public void actionPerformed(ActionEvent e)
988 copy_actionPerformed(e);
991 addMenuActionAndAccelerator(keyStroke, copy, al);
993 cut.setText(MessageManager.getString("action.cut"));
994 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
995 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
996 al = new ActionListener()
999 public void actionPerformed(ActionEvent e)
1001 cut_actionPerformed(e);
1004 addMenuActionAndAccelerator(keyStroke, cut, al);
1006 JMenuItem delete = new JMenuItem(
1007 MessageManager.getString("action.delete"));
1008 delete.addActionListener(new ActionListener()
1011 public void actionPerformed(ActionEvent e)
1013 delete_actionPerformed(e);
1017 pasteMenu.setText(MessageManager.getString("action.paste"));
1018 JMenuItem pasteNew = new JMenuItem(
1019 MessageManager.getString("label.to_new_alignment"));
1020 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1021 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1022 | KeyEvent.SHIFT_MASK,
1024 al = new ActionListener()
1027 public void actionPerformed(ActionEvent e)
1031 pasteNew_actionPerformed(e);
1032 } catch (IOException | InterruptedException e1)
1034 // TODO Auto-generated catch block
1035 e1.printStackTrace();
1039 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1041 JMenuItem pasteThis = new JMenuItem(
1042 MessageManager.getString("label.to_this_alignment"));
1043 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1044 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1045 al = new ActionListener()
1048 public void actionPerformed(ActionEvent e)
1052 pasteThis_actionPerformed(e);
1053 } catch (IOException | InterruptedException e1)
1055 // TODO Auto-generated catch block
1056 e1.printStackTrace();
1060 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1062 JMenuItem createPNG = new JMenuItem("PNG");
1063 createPNG.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1071 createPNG.setActionCommand(
1072 MessageManager.getString("label.save_png_image"));
1073 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1074 font.addActionListener(new ActionListener()
1077 public void actionPerformed(ActionEvent e)
1079 font_actionPerformed(e);
1083 MessageManager.getString("label.show_sequence_limits"));
1084 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1085 seqLimits.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 seqLimit_actionPerformed(e);
1093 JMenuItem epsFile = new JMenuItem("EPS");
1094 epsFile.addActionListener(new ActionListener()
1097 public void actionPerformed(ActionEvent e)
1103 JMenuItem createSVG = new JMenuItem("SVG");
1104 createSVG.addActionListener(new ActionListener()
1107 public void actionPerformed(ActionEvent e)
1113 JMenuItem loadTreeMenuItem = new JMenuItem(
1114 MessageManager.getString("label.load_associated_tree"));
1115 loadTreeMenuItem.setActionCommand(
1116 MessageManager.getString("label.load_tree_for_sequence_set"));
1117 loadTreeMenuItem.addActionListener(new ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 loadTreeMenuItem_actionPerformed(e);
1126 scaleAbove.setVisible(false);
1127 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1128 scaleAbove.addActionListener(new ActionListener()
1131 public void actionPerformed(ActionEvent e)
1133 scaleAbove_actionPerformed(e);
1136 scaleLeft.setVisible(false);
1137 scaleLeft.setSelected(true);
1138 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1139 scaleLeft.addActionListener(new ActionListener()
1142 public void actionPerformed(ActionEvent e)
1144 scaleLeft_actionPerformed(e);
1147 scaleRight.setVisible(false);
1148 scaleRight.setSelected(true);
1149 scaleRight.setText(MessageManager.getString("action.scale_right"));
1150 scaleRight.addActionListener(new ActionListener()
1153 public void actionPerformed(ActionEvent e)
1155 scaleRight_actionPerformed(e);
1158 centreColumnLabelsMenuItem.setVisible(true);
1159 centreColumnLabelsMenuItem.setState(false);
1160 centreColumnLabelsMenuItem.setText(
1161 MessageManager.getString("label.centre_column_labels"));
1162 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1165 public void actionPerformed(ActionEvent e)
1167 centreColumnLabels_actionPerformed(e);
1170 followHighlightMenuItem.setVisible(true);
1171 followHighlightMenuItem.setState(true);
1172 followHighlightMenuItem
1173 .setText(MessageManager.getString("label.automatic_scrolling"));
1174 followHighlightMenuItem.addActionListener(new ActionListener()
1178 public void actionPerformed(ActionEvent e)
1180 followHighlight_actionPerformed();
1186 .setText(MessageManager.getString("action.by_tree_order"));
1187 sort.setText(MessageManager.getString("action.sort"));
1188 sort.addMenuListener(new MenuListener()
1191 public void menuSelected(MenuEvent e)
1193 buildTreeSortMenu();
1197 public void menuDeselected(MenuEvent e)
1202 public void menuCanceled(MenuEvent e)
1207 .setText(MessageManager.getString("label.sort_by_score"));
1208 sort.add(sortByAnnotScore);
1209 sort.addMenuListener(new javax.swing.event.MenuListener()
1213 public void menuCanceled(MenuEvent e)
1218 public void menuDeselected(MenuEvent e)
1223 public void menuSelected(MenuEvent e)
1225 buildSortByAnnotationScoresMenu();
1228 sortByAnnotScore.setVisible(false);
1231 .setText(MessageManager.getString("action.calculate_tree_pca"));
1233 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1235 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1236 padGapsMenuitem.addActionListener(new ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 padGapsMenuitem_actionPerformed(e);
1244 JMenuItem vamsasStore = new JMenuItem(
1245 MessageManager.getString("label.vamsas_store"));
1246 vamsasStore.setVisible(false);
1247 vamsasStore.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 vamsasStore_actionPerformed(e);
1256 .setText(MessageManager.getString("label.translate_cDNA"));
1257 showTranslation.addActionListener(new ActionListener()
1260 public void actionPerformed(ActionEvent e)
1262 showTranslation_actionPerformed(e);
1265 showReverse.setText(MessageManager.getString("label.reverse"));
1266 showReverse.addActionListener(new ActionListener()
1269 public void actionPerformed(ActionEvent e)
1271 showReverse_actionPerformed(false);
1274 showReverseComplement
1275 .setText(MessageManager.getString("label.reverse_complement"));
1276 showReverseComplement.addActionListener(new ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 showReverse_actionPerformed(true);
1285 JMenuItem extractScores = new JMenuItem(
1286 MessageManager.getString("label.extract_scores"));
1287 extractScores.addActionListener(new ActionListener()
1290 public void actionPerformed(ActionEvent e)
1292 extractScores_actionPerformed(e);
1295 extractScores.setVisible(true);
1296 // JBPNote: TODO: make gui for regex based score extraction
1298 // for show products actions see AlignFrame.canShowProducts
1299 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1301 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1302 runGroovy.setToolTipText(
1303 MessageManager.getString("label.run_groovy_tip"));
1304 runGroovy.addActionListener(new ActionListener()
1307 public void actionPerformed(ActionEvent e)
1309 runGroovy_actionPerformed();
1313 JMenuItem openFeatureSettings = new JMenuItem(
1314 MessageManager.getString("action.feature_settings"));
1315 openFeatureSettings.addActionListener(new ActionListener()
1318 public void actionPerformed(ActionEvent e)
1320 featureSettings_actionPerformed(e);
1323 JMenuItem fetchSequence = new JMenuItem(
1324 MessageManager.getString("label.fetch_sequences"));
1325 fetchSequence.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 fetchSequence_actionPerformed(e);
1334 JMenuItem associatedData = new JMenuItem(
1335 MessageManager.getString("label.load_features_annotations"));
1336 associatedData.addActionListener(new ActionListener()
1339 public void actionPerformed(ActionEvent e)
1343 associatedData_actionPerformed(e);
1344 } catch (IOException | InterruptedException e1)
1346 // TODO Auto-generated catch block
1347 e1.printStackTrace();
1351 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1352 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1353 loadVcf.addActionListener(new ActionListener()
1356 public void actionPerformed(ActionEvent e)
1358 loadVcf_actionPerformed();
1361 autoCalculate.setText(
1362 MessageManager.getString("label.autocalculate_consensus"));
1363 autoCalculate.setState(
1364 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1365 autoCalculate.addActionListener(new ActionListener()
1368 public void actionPerformed(ActionEvent e)
1370 autoCalculate_actionPerformed(e);
1374 MessageManager.getString("label.sort_alignment_new_tree"));
1375 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1376 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1378 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1379 sortByTree.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 sortByTreeOption_actionPerformed(e);
1388 listenToViewSelections.setText(
1389 MessageManager.getString("label.listen_for_selections"));
1390 listenToViewSelections
1391 .setToolTipText("<html>" + MessageManager.getString(
1392 "label.selections_mirror_selections_made_same_sequences_other_views"));
1393 listenToViewSelections.setState(false);
1394 listenToViewSelections.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 listenToViewSelections_actionPerformed(e);
1403 JMenu addSequenceMenu = new JMenu(
1404 MessageManager.getString("label.add_sequences"));
1405 JMenuItem addFromFile = new JMenuItem(
1406 MessageManager.getString("label.from_file"));
1407 addFromFile.addActionListener(new ActionListener()
1410 public void actionPerformed(ActionEvent e)
1412 addFromFile_actionPerformed(e);
1415 JMenuItem addFromText = new JMenuItem(
1416 MessageManager.getString("label.from_textbox"));
1417 addFromText.addActionListener(new ActionListener()
1420 public void actionPerformed(ActionEvent e)
1422 addFromText_actionPerformed(e);
1425 JMenuItem addFromURL = new JMenuItem(
1426 MessageManager.getString("label.from_url"));
1427 addFromURL.addActionListener(new ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 addFromURL_actionPerformed(e);
1435 JMenuItem exportFeatures = new JMenuItem(
1436 MessageManager.getString("label.export_features"));
1437 exportFeatures.addActionListener(new ActionListener()
1440 public void actionPerformed(ActionEvent e)
1442 exportFeatures_actionPerformed(e);
1445 JMenuItem exportAnnotations = new JMenuItem(
1446 MessageManager.getString("label.export_annotations"));
1447 exportAnnotations.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 exportAnnotations_actionPerformed(e);
1455 statusPanel.setLayout(new GridLayout());
1456 JMenuItem showAllSeqs = new JMenuItem(
1457 MessageManager.getString("label.all_sequences"));
1458 showAllSeqs.setToolTipText(
1459 MessageManager.getString("label.toggle_sequence_visibility"));
1460 showAllSeqs.addActionListener(new ActionListener()
1463 public void actionPerformed(ActionEvent e)
1465 showAllSeqs_actionPerformed(e);
1468 JMenuItem showAllColumns = new JMenuItem(
1469 MessageManager.getString("label.all_columns"));
1470 showAllColumns.setToolTipText(
1471 MessageManager.getString("label.toggle_columns_visibility"));
1472 showAllColumns.addActionListener(new ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 showAllColumns_actionPerformed(e);
1480 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1481 JMenuItem hideSelSequences = new JMenuItem(
1482 MessageManager.getString("label.selected_sequences"));
1483 hideSelSequences.setToolTipText(
1484 MessageManager.getString("label.toggle_sequence_visibility"));
1485 hideSelSequences.addActionListener(new ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 hideSelSequences_actionPerformed(e);
1493 JMenuItem hideSelColumns = new JMenuItem(
1494 MessageManager.getString("label.selected_columns"));
1495 hideSelColumns.setToolTipText(
1496 MessageManager.getString("label.toggle_columns_visibility"));
1497 hideSelColumns.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent e)
1502 hideSelColumns_actionPerformed(e);
1505 JMenuItem hideAllSelection = new JMenuItem(
1506 MessageManager.getString("label.selected_region"));
1507 hideAllSelection.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 hideAllSelection_actionPerformed(e);
1515 // TODO: should be hidden if no selection exists.
1516 JMenuItem hideAllButSelection = new JMenuItem(
1517 MessageManager.getString("label.all_but_selected_region"));
1518 hideAllButSelection.addActionListener(new ActionListener()
1521 public void actionPerformed(ActionEvent e)
1523 hideAllButSelection_actionPerformed(e);
1526 JMenuItem showAllhidden = new JMenuItem(
1527 MessageManager.getString("label.all_sequences_columns"));
1528 showAllhidden.setToolTipText(MessageManager
1529 .getString("label.toggles_visibility_hidden_selected_regions"));
1530 showAllhidden.addActionListener(new ActionListener()
1533 public void actionPerformed(ActionEvent e)
1535 showAllhidden_actionPerformed(e);
1538 hiddenMarkers.setText(
1539 MessageManager.getString("action.show_hidden_markers"));
1540 hiddenMarkers.addActionListener(new ActionListener()
1543 public void actionPerformed(ActionEvent e)
1545 hiddenMarkers_actionPerformed(e);
1549 JMenuItem invertColSel = new JMenuItem(
1550 MessageManager.getString("action.invert_column_selection"));
1551 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1552 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1553 | KeyEvent.ALT_MASK,
1555 al = new ActionListener()
1558 public void actionPerformed(ActionEvent e)
1560 invertColSel_actionPerformed(e);
1563 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1565 showComplementMenuItem.setVisible(false);
1566 showComplementMenuItem.addActionListener(new ActionListener()
1569 public void actionPerformed(ActionEvent e)
1571 showComplement_actionPerformed(showComplementMenuItem.getState());
1575 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1578 public void stateChanged(ChangeEvent evt)
1580 JTabbedPane pane = (JTabbedPane) evt.getSource();
1581 int sel = pane.getSelectedIndex();
1582 tabSelectionChanged(sel);
1585 tabbedPane.addMouseListener(new MouseAdapter()
1588 public void mousePressed(MouseEvent e)
1590 if (e.isPopupTrigger()) // Mac
1592 tabbedPane_mousePressed(e);
1597 public void mouseReleased(MouseEvent e)
1599 if (e.isPopupTrigger()) // Windows
1601 tabbedPane_mousePressed(e);
1605 tabbedPane.addFocusListener(new FocusAdapter()
1608 public void focusGained(FocusEvent e)
1610 tabbedPane_focusGained(e);
1614 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1615 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1616 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1617 al = new ActionListener()
1620 public void actionPerformed(ActionEvent e)
1622 save_actionPerformed(e);
1625 addMenuActionAndAccelerator(keyStroke, save, al);
1627 reload.setEnabled(false);
1628 reload.setText(MessageManager.getString("action.reload"));
1629 reload.addActionListener(new ActionListener()
1632 public void actionPerformed(ActionEvent e)
1634 reload_actionPerformed(e);
1638 JMenuItem newView = new JMenuItem(
1639 MessageManager.getString("action.new_view"));
1640 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1641 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1642 al = new ActionListener()
1645 public void actionPerformed(ActionEvent e)
1647 newView_actionPerformed(e);
1650 addMenuActionAndAccelerator(keyStroke, newView, al);
1652 tabbedPane.setToolTipText("<html><i>"
1653 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1656 formatMenu.setText(MessageManager.getString("action.format"));
1657 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1659 idRightAlign.setText(
1660 MessageManager.getString("label.right_align_sequence_id"));
1661 idRightAlign.addActionListener(new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 idRightAlign_actionPerformed(e);
1670 gatherViews.setEnabled(false);
1671 gatherViews.setText(MessageManager.getString("action.gather_views"));
1672 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1673 al = new ActionListener()
1676 public void actionPerformed(ActionEvent e)
1678 gatherViews_actionPerformed(e);
1681 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1683 expandViews.setEnabled(false);
1684 expandViews.setText(MessageManager.getString("action.expand_views"));
1685 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1686 al = new ActionListener()
1689 public void actionPerformed(ActionEvent e)
1691 expandViews_actionPerformed(e);
1694 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1696 JMenuItem pageSetup = new JMenuItem(
1697 MessageManager.getString("action.page_setup"));
1698 pageSetup.addActionListener(new ActionListener()
1701 public void actionPerformed(ActionEvent e)
1703 pageSetup_actionPerformed(e);
1706 JMenuItem alignmentProperties = new JMenuItem(
1707 MessageManager.getString("label.alignment_props"));
1708 alignmentProperties.addActionListener(new ActionListener()
1711 public void actionPerformed(ActionEvent actionEvent)
1713 alignmentProperties();
1716 JMenuItem selectHighlighted = new JMenuItem(
1717 MessageManager.getString("action.select_highlighted_columns"));
1718 selectHighlighted.setToolTipText(
1719 MessageManager.getString("tooltip.select_highlighted_columns"));
1720 al = new ActionListener()
1723 public void actionPerformed(ActionEvent actionEvent)
1725 selectHighlightedColumns_actionPerformed(actionEvent);
1728 selectHighlighted.addActionListener(al);
1729 JMenu tooltipSettingsMenu = new JMenu(
1730 MessageManager.getString("label.sequence_id_tooltip"));
1731 JMenu autoAnnMenu = new JMenu(
1732 MessageManager.getString("label.autocalculated_annotation"));
1734 JMenu exportImageMenu = new JMenu(
1735 MessageManager.getString("label.export_image"));
1736 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1737 alignFrameMenuBar.add(fileMenu);
1738 alignFrameMenuBar.add(editMenu);
1739 alignFrameMenuBar.add(selectMenu);
1740 alignFrameMenuBar.add(viewMenu);
1741 alignFrameMenuBar.add(annotationsMenu);
1742 alignFrameMenuBar.add(formatMenu);
1743 alignFrameMenuBar.add(colourMenu);
1744 alignFrameMenuBar.add(calculateMenu);
1745 alignFrameMenuBar.add(webService);
1746 alignFrameMenuBar.add(hmmerMenu);
1748 fileMenu.add(fetchSequence);
1749 fileMenu.add(addSequenceMenu);
1750 fileMenu.add(reload);
1751 fileMenu.addSeparator();
1752 fileMenu.add(vamsasStore);
1754 fileMenu.add(saveAs);
1755 fileMenu.add(outputTextboxMenu);
1756 fileMenu.add(pageSetup);
1757 fileMenu.add(printMenuItem);
1758 fileMenu.addSeparator();
1759 fileMenu.add(exportImageMenu);
1760 fileMenu.add(exportFeatures);
1761 fileMenu.add(exportAnnotations);
1762 fileMenu.add(loadTreeMenuItem);
1763 fileMenu.add(associatedData);
1764 fileMenu.add(loadVcf);
1765 fileMenu.addSeparator();
1766 fileMenu.add(closeMenuItem);
1768 pasteMenu.add(pasteNew);
1769 pasteMenu.add(pasteThis);
1770 editMenu.add(undoMenuItem);
1771 editMenu.add(redoMenuItem);
1774 editMenu.add(pasteMenu);
1775 editMenu.add(delete);
1776 editMenu.addSeparator();
1777 editMenu.add(remove2LeftMenuItem);
1778 editMenu.add(remove2RightMenuItem);
1779 editMenu.add(removeGappedColumnMenuItem);
1780 editMenu.add(removeAllGapsMenuItem);
1781 editMenu.add(removeRedundancyMenuItem);
1782 editMenu.addSeparator();
1783 // dont add these yet in the CVS build - they cannot be undone!
1784 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1785 // editMenu.add(justifyLeftMenuItem);
1786 // editMenu.add(justifyRightMenuItem);
1787 // editMenu.addSeparator();
1788 editMenu.add(padGapsMenuitem);
1790 showMenu.add(showAllColumns);
1791 showMenu.add(showAllSeqs);
1792 showMenu.add(showAllhidden);
1793 hideMenu.add(hideSelColumns);
1794 hideMenu.add(hideSelSequences);
1795 hideMenu.add(hideAllSelection);
1796 hideMenu.add(hideAllButSelection);
1797 viewMenu.add(newView);
1798 viewMenu.add(expandViews);
1799 viewMenu.add(gatherViews);
1800 viewMenu.addSeparator();
1801 viewMenu.add(showMenu);
1802 viewMenu.add(hideMenu);
1803 viewMenu.add(showComplementMenuItem);
1804 viewMenu.addSeparator();
1805 viewMenu.add(followHighlightMenuItem);
1806 viewMenu.addSeparator();
1807 viewMenu.add(showSeqFeatures);
1808 // viewMenu.add(showSeqFeaturesHeight);
1809 viewMenu.add(openFeatureSettings);
1810 tooltipSettingsMenu.add(showDbRefsMenuitem);
1811 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1812 viewMenu.add(tooltipSettingsMenu);
1813 viewMenu.addSeparator();
1814 viewMenu.add(alignmentProperties);
1815 viewMenu.addSeparator();
1816 viewMenu.add(overviewMenuItem);
1818 annotationsMenu.add(annotationPanelMenuItem);
1819 annotationsMenu.addSeparator();
1820 annotationsMenu.add(showAllAlAnnotations);
1821 annotationsMenu.add(hideAllAlAnnotations);
1822 annotationsMenu.addSeparator();
1823 annotationsMenu.add(showAllSeqAnnotations);
1824 annotationsMenu.add(hideAllSeqAnnotations);
1825 annotationsMenu.add(sortAnnBySequence);
1826 annotationsMenu.add(sortAnnByLabel);
1827 annotationsMenu.addSeparator();
1828 autoAnnMenu.add(showAutoFirst);
1829 autoAnnMenu.add(showAutoLast);
1830 autoAnnMenu.addSeparator();
1831 autoAnnMenu.add(applyAutoAnnotationSettings);
1832 autoAnnMenu.add(showConsensusHistogram);
1833 autoAnnMenu.add(showSequenceLogo);
1834 autoAnnMenu.add(normaliseSequenceLogo);
1835 autoAnnMenu.addSeparator();
1836 autoAnnMenu.add(showGroupConservation);
1837 autoAnnMenu.add(showGroupConsensus);
1838 annotationsMenu.add(autoAnnMenu);
1840 sort.add(sortIDMenuItem);
1841 sort.add(sortLengthMenuItem);
1842 sort.add(sortGroupMenuItem);
1843 sort.add(sortPairwiseMenuItem);
1844 sort.add(sortByTreeMenu);
1845 calculateMenu.add(sort);
1846 calculateMenu.add(calculateTree);
1847 calculateMenu.addSeparator();
1848 calculateMenu.add(pairwiseAlignmentMenuItem);
1849 calculateMenu.addSeparator();
1850 calculateMenu.add(showTranslation);
1851 calculateMenu.add(showReverse);
1852 calculateMenu.add(showReverseComplement);
1853 calculateMenu.add(showProducts);
1854 calculateMenu.add(autoCalculate);
1855 calculateMenu.add(sortByTree);
1856 calculateMenu.addSeparator();
1857 calculateMenu.add(expandAlignment);
1858 calculateMenu.add(extractScores);
1859 calculateMenu.addSeparator();
1860 calculateMenu.add(runGroovy);
1862 webServiceNoServices = new JMenuItem(
1863 MessageManager.getString("label.no_services"));
1864 webService.add(webServiceNoServices);
1865 exportImageMenu.add(htmlMenuItem);
1866 exportImageMenu.add(epsFile);
1867 exportImageMenu.add(createPNG);
1868 exportImageMenu.add(createBioJS);
1869 exportImageMenu.add(createSVG);
1870 addSequenceMenu.add(addFromFile);
1871 addSequenceMenu.add(addFromText);
1872 addSequenceMenu.add(addFromURL);
1873 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1874 statusPanel.add(statusBar, null);
1875 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1877 formatMenu.add(font);
1878 formatMenu.addSeparator();
1879 formatMenu.add(wrapMenuItem);
1880 formatMenu.add(scaleAbove);
1881 formatMenu.add(scaleLeft);
1882 formatMenu.add(scaleRight);
1883 formatMenu.add(seqLimits);
1884 formatMenu.add(idRightAlign);
1885 formatMenu.add(hiddenMarkers);
1886 formatMenu.add(viewBoxesMenuItem);
1887 formatMenu.add(viewTextMenuItem);
1888 formatMenu.add(colourTextMenuItem);
1889 formatMenu.add(renderGapsMenuItem);
1890 formatMenu.add(centreColumnLabelsMenuItem);
1891 formatMenu.add(showNonconservedMenuItem);
1892 selectMenu.add(findMenuItem);
1893 selectMenu.addSeparator();
1894 selectMenu.add(selectAllSequenceMenuItem);
1895 selectMenu.add(deselectAllSequenceMenuItem);
1896 selectMenu.add(invertSequenceMenuItem);
1897 selectMenu.add(invertColSel);
1898 selectMenu.add(createGroup);
1899 selectMenu.add(unGroup);
1900 selectMenu.add(grpsFromSelection);
1901 selectMenu.add(deleteGroups);
1902 selectMenu.add(annotationColumn);
1903 selectMenu.add(selectHighlighted);
1904 // TODO - determine if the listenToViewSelections button is needed : see bug
1906 // selectMenu.addSeparator();
1907 // selectMenu.add(listenToViewSelections);
1911 * Constructs the entries on the HMMER menu
1913 protected void initHMMERMenu()
1918 JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
1919 JMenuItem hmmBuildSettings = new JMenuItem(
1920 MessageManager.getString("label.edit_settings_and_run"));
1921 hmmBuildSettings.addActionListener(new ActionListener()
1924 public void actionPerformed(ActionEvent e)
1926 hmmBuild_actionPerformed(false);
1929 JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
1930 "label.action_with_default_settings", "hmmbuild"));
1931 hmmBuildRun.addActionListener(new ActionListener()
1934 public void actionPerformed(ActionEvent e)
1936 hmmBuild_actionPerformed(true);
1939 hmmBuild.add(hmmBuildRun);
1940 hmmBuild.add(hmmBuildSettings);
1945 JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
1946 JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
1947 "label.action_with_default_settings", "hmmalign"));
1948 hmmAlignRun.addActionListener(new ActionListener()
1951 public void actionPerformed(ActionEvent e)
1953 hmmAlign_actionPerformed(true);
1956 JMenuItem hmmAlignSettings = new JMenuItem(
1957 MessageManager.getString("label.edit_settings_and_run"));
1958 hmmAlignSettings.addActionListener(new ActionListener()
1961 public void actionPerformed(ActionEvent e)
1963 hmmAlign_actionPerformed(false);
1966 hmmAlign.add(hmmAlignRun);
1967 hmmAlign.add(hmmAlignSettings);
1972 JMenu hmmSearch = new JMenu(
1973 MessageManager.getString("label.hmmsearch"));
1974 JMenuItem hmmSearchSettings = new JMenuItem(
1975 MessageManager.getString("label.edit_settings_and_run"));
1976 hmmSearchSettings.addActionListener(new ActionListener()
1979 public void actionPerformed(ActionEvent e)
1981 hmmSearch_actionPerformed(false);
1984 JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
1985 "label.action_with_default_settings", "hmmsearch"));
1986 hmmSearchRun.addActionListener(new ActionListener()
1989 public void actionPerformed(ActionEvent e)
1991 hmmSearch_actionPerformed(true);
1994 JMenuItem addDatabase = new JMenuItem(
1995 MessageManager.getString("label.add_database"));
1996 addDatabase.addActionListener(new ActionListener()
1999 public void actionPerformed(ActionEvent e)
2003 addDatabase_actionPerformed();
2004 } catch (IOException e1)
2006 e1.printStackTrace();
2010 hmmSearch.add(hmmSearchRun);
2011 hmmSearch.add(hmmSearchSettings);
2012 // hmmSearch.add(addDatabase);
2017 hmmerMenu.setText(MessageManager.getString("action.hmmer"));
2018 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
2019 hmmerMenu.add(hmmBuild);
2020 hmmerMenu.add(hmmAlign);
2021 hmmerMenu.add(hmmSearch);
2025 protected void loadVcf_actionPerformed()
2030 * Constructs the entries on the Colour menu (but does not add them to the
2033 protected void initColourMenu()
2035 applyToAllGroups = new JCheckBoxMenuItem(
2036 MessageManager.getString("label.apply_colour_to_all_groups"));
2037 applyToAllGroups.addActionListener(new ActionListener()
2040 public void actionPerformed(ActionEvent e)
2042 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2046 textColour = new JMenuItem(
2047 MessageManager.getString("label.text_colour"));
2048 textColour.addActionListener(new ActionListener()
2051 public void actionPerformed(ActionEvent e)
2053 textColour_actionPerformed();
2057 conservationMenuItem = new JCheckBoxMenuItem(
2058 MessageManager.getString("action.by_conservation"));
2059 conservationMenuItem.addActionListener(new ActionListener()
2062 public void actionPerformed(ActionEvent e)
2064 conservationMenuItem_actionPerformed(
2065 conservationMenuItem.isSelected());
2069 abovePIDThreshold = new JCheckBoxMenuItem(
2070 MessageManager.getString("label.above_identity_threshold"));
2071 abovePIDThreshold.addActionListener(new ActionListener()
2074 public void actionPerformed(ActionEvent e)
2076 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2079 modifyPID = new JMenuItem(
2080 MessageManager.getString("label.modify_identity_threshold"));
2081 modifyPID.addActionListener(new ActionListener()
2084 public void actionPerformed(ActionEvent e)
2086 modifyPID_actionPerformed();
2089 modifyConservation = new JMenuItem(MessageManager
2090 .getString("label.modify_conservation_threshold"));
2091 modifyConservation.addActionListener(new ActionListener()
2094 public void actionPerformed(ActionEvent e)
2096 modifyConservation_actionPerformed();
2100 annotationColour = new JMenuItem(
2101 MessageManager.getString("action.by_annotation"));
2102 annotationColour.addActionListener(new ActionListener()
2105 public void actionPerformed(ActionEvent e)
2107 annotationColour_actionPerformed();
2112 protected void selectHighlightedColumns_actionPerformed(
2113 ActionEvent actionEvent)
2115 // TODO Auto-generated method stub
2120 * Generate the reverse sequence (or reverse complement if the flag is true)
2121 * and add it to the alignment
2125 protected void showReverse_actionPerformed(boolean complement)
2130 * Try to run script in a Groovy console, having first ensured that this
2131 * alignframe is set as currentAlignFrame in Desktop
2133 protected void runGroovy_actionPerformed()
2139 * Adds the given action listener and key accelerator to the given menu item.
2140 * Also saves in a lookup table to support lookup of action by key stroke.
2144 * @param actionListener
2146 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2147 JMenuItem menuItem, ActionListener actionListener)
2149 menuItem.setAccelerator(keyStroke);
2150 accelerators.put(keyStroke, menuItem);
2151 menuItem.addActionListener(actionListener);
2155 * Action on clicking sort annotations by type.
2159 protected void sortAnnotations_actionPerformed()
2164 * Action on clicking Show all annotations.
2166 * @param forSequences
2167 * update sequence-related annotations
2168 * @param forAlignment
2169 * update non-sequence-related annotations
2171 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2172 boolean forAlignment)
2174 setAnnotationsVisibility(true, forSequences, forAlignment);
2178 * Action on clicking Hide all annotations.
2180 * @param forSequences
2181 * update sequence-related annotations
2182 * @param forAlignment
2183 * update non-sequence-related annotations
2185 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2186 boolean forAlignment)
2188 setAnnotationsVisibility(false, forSequences, forAlignment);
2192 * Set the visibility of annotations to true or false. Can act on
2193 * sequence-related annotations, or alignment-related, or both.
2196 * @param forSequences
2197 * update sequence-related annotations
2198 * @param forAlignment
2199 * update non-sequence-related annotations
2201 protected void setAnnotationsVisibility(boolean visible,
2202 boolean forSequences, boolean forAlignment)
2207 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2209 // TODO Auto-generated method stub
2213 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2215 // TODO Auto-generated method stub
2219 protected void showAllhidden_actionPerformed(ActionEvent e)
2221 // TODO Auto-generated method stub
2225 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2227 // TODO Auto-generated method stub
2231 protected void hideAllSelection_actionPerformed(ActionEvent e)
2233 // TODO Auto-generated method stub
2237 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2239 // TODO Auto-generated method stub
2243 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2245 // TODO Auto-generated method stub
2249 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2251 // TODO Auto-generated method stub
2255 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2257 // TODO Auto-generated method stub
2261 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2263 // TODO Auto-generated method stub
2267 protected void showGroupConservation_actionPerformed(ActionEvent e)
2269 // TODO Auto-generated method stub
2273 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2275 // TODO Auto-generated method stub
2279 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2281 // TODO Auto-generated method stub
2285 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2287 // TODO Auto-generated method stub
2291 protected void followHighlight_actionPerformed()
2293 // TODO Auto-generated method stub
2297 protected void showNpFeats_actionPerformed(ActionEvent e)
2299 // TODO Auto-generated method stub
2303 protected void showDbRefs_actionPerformed(ActionEvent e)
2305 // TODO Auto-generated method stub
2309 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2313 protected void buildSortByAnnotationScoresMenu()
2317 protected void extractScores_actionPerformed(ActionEvent e)
2321 protected void outputText_actionPerformed(ActionEvent e)
2325 public void addFromFile_actionPerformed(ActionEvent e)
2330 public void addFromText_actionPerformed(ActionEvent e)
2335 public void addFromURL_actionPerformed(ActionEvent e)
2340 public void exportFeatures_actionPerformed(ActionEvent e)
2345 public void exportAnnotations_actionPerformed(ActionEvent e)
2350 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2354 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2359 protected void closeMenuItem_actionPerformed(boolean b)
2363 protected void redoMenuItem_actionPerformed(ActionEvent e)
2367 protected void undoMenuItem_actionPerformed(ActionEvent e)
2371 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2375 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2379 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2383 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2387 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2391 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2395 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2399 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2403 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2407 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2411 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2415 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2419 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2423 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2427 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2431 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2435 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2439 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2443 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2447 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2451 protected void conservationMenuItem_actionPerformed(boolean selected)
2455 protected void printMenuItem_actionPerformed(ActionEvent e)
2459 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2463 protected void findMenuItem_actionPerformed(ActionEvent e)
2467 protected void abovePIDThreshold_actionPerformed(boolean selected)
2471 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2475 protected void deleteGroups_actionPerformed(ActionEvent e)
2479 protected void createGroup_actionPerformed(ActionEvent e)
2483 protected void unGroup_actionPerformed(ActionEvent e)
2487 protected void copy_actionPerformed(ActionEvent e)
2491 protected void cut_actionPerformed(ActionEvent e)
2495 protected void delete_actionPerformed(ActionEvent e)
2499 protected void pasteNew_actionPerformed(ActionEvent e)
2500 throws IOException, InterruptedException
2504 protected void pasteThis_actionPerformed(ActionEvent e)
2505 throws IOException, InterruptedException
2509 protected void applyToAllGroups_actionPerformed(boolean selected)
2513 protected void hmmBuild_actionPerformed(boolean withDefaults)
2517 protected void hmmSearch_actionPerformed(boolean withDefaults)
2521 protected void addDatabase_actionPerformed()
2522 throws FileFormatException, IOException
2526 protected void hmmAlign_actionPerformed(boolean withDefaults)
2530 public void createPNG(java.io.File f)
2534 protected void font_actionPerformed(ActionEvent e)
2538 protected void seqLimit_actionPerformed(ActionEvent e)
2542 public void seqDBRef_actionPerformed(ActionEvent e)
2547 public void createEPS(java.io.File f)
2551 public void createSVG(java.io.File f)
2556 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2562 * Template method to handle the 'load T-Coffee scores' menu event.
2564 * Subclasses override this method to provide a custom action.
2569 protected void loadScores_actionPerformed(ActionEvent event)
2574 protected void jpred_actionPerformed(ActionEvent e)
2578 protected void scaleAbove_actionPerformed(ActionEvent e)
2582 protected void scaleLeft_actionPerformed(ActionEvent e)
2586 protected void scaleRight_actionPerformed(ActionEvent e)
2590 protected void modifyPID_actionPerformed()
2594 protected void modifyConservation_actionPerformed()
2598 protected void saveAs_actionPerformed(ActionEvent e)
2602 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2606 public void vamsasStore_actionPerformed(ActionEvent e)
2611 public void vamsasLoad_actionPerformed(ActionEvent e)
2616 public void showTranslation_actionPerformed(ActionEvent e)
2621 public void featureSettings_actionPerformed(ActionEvent e)
2626 public void fetchSequence_actionPerformed(ActionEvent e)
2631 public void smoothFont_actionPerformed(ActionEvent e)
2636 public void annotationColour_actionPerformed()
2640 public void annotationColumn_actionPerformed(ActionEvent e)
2644 public void associatedData_actionPerformed(ActionEvent e)
2645 throws IOException, InterruptedException
2650 public void autoCalculate_actionPerformed(ActionEvent e)
2655 public void sortByTreeOption_actionPerformed(ActionEvent e)
2660 public void showAllSeqs_actionPerformed(ActionEvent e)
2665 public void showAllColumns_actionPerformed(ActionEvent e)
2670 public void hideSelSequences_actionPerformed(ActionEvent e)
2675 public void hideSelColumns_actionPerformed(ActionEvent e)
2680 public void hiddenMarkers_actionPerformed(ActionEvent e)
2685 public void findPdbId_actionPerformed(ActionEvent e)
2690 public void enterPdbId_actionPerformed(ActionEvent e)
2695 public void pdbFile_actionPerformed(ActionEvent e)
2700 public void invertColSel_actionPerformed(ActionEvent e)
2705 public void tabSelectionChanged(int sel)
2710 public void tabbedPane_mousePressed(MouseEvent e)
2715 public void tabbedPane_focusGained(FocusEvent e)
2720 public void save_actionPerformed(ActionEvent e)
2725 public void reload_actionPerformed(ActionEvent e)
2730 public void newView_actionPerformed(ActionEvent e)
2735 public void textColour_actionPerformed()
2740 public void idRightAlign_actionPerformed(ActionEvent e)
2745 public void expandViews_actionPerformed(ActionEvent e)
2750 public void gatherViews_actionPerformed(ActionEvent e)
2755 public void buildTreeSortMenu()
2760 public void pageSetup_actionPerformed(ActionEvent e)
2765 public void alignmentProperties()
2770 protected void expand_newalign(ActionEvent e)
2772 // TODO Auto-generated method stub
2776 protected boolean isShowAutoCalculatedAbove()
2778 return showAutoCalculatedAbove;
2781 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2783 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2786 protected SequenceAnnotationOrder getAnnotationSortOrder()
2788 return annotationSortOrder;
2791 protected void setAnnotationSortOrder(
2792 SequenceAnnotationOrder annotationSortOrder)
2794 this.annotationSortOrder = annotationSortOrder;
2797 public Map<KeyStroke, JMenuItem> getAccelerators()
2799 return this.accelerators;
2803 * Returns the selected index of the tabbed pane, or -1 if none selected
2804 * (including the case where the tabbed pane has not been made visible).
2808 public int getTabIndex()
2810 return tabbedPane.getSelectedIndex();
2813 public JPanel getStatusPanel()
2819 * Sets a reference to the containing split frame. Also makes the 'toggle
2820 * split view' menu item visible and checked.
2824 public void setSplitFrame(SplitContainerI sf)
2826 this.splitFrame = sf;
2829 this.showComplementMenuItem.setVisible(true);
2830 this.showComplementMenuItem.setState(true);
2834 public SplitContainerI getSplitViewContainer()
2836 return this.splitFrame;
2839 protected void showComplement_actionPerformed(boolean complement)