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 JMenu hmmAlign = new JMenu();
77 protected JMenuItem hmmAlignRun = new JMenuItem();
79 protected JMenuItem hmmAlignSettings = new JMenuItem();
81 protected JMenu hmmSearch = new JMenu();
83 protected JMenuItem hmmSearchRun = new JMenuItem();
85 protected JMenuItem hmmSearchSettings = new JMenuItem();
87 protected JMenuItem addDatabase = new JMenuItem();
89 protected JMenu hmmBuild = new JMenu();
91 protected JMenuItem hmmBuildRun = new JMenuItem();
93 protected JMenuItem hmmBuildSettings = new JMenuItem();
95 protected JMenuItem webServiceNoServices;
97 protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
99 protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
101 protected JMenu sortByAnnotScore = new JMenu();
103 public JLabel statusBar = new JLabel();
105 protected JMenu outputTextboxMenu = new JMenu();
107 protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
109 protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
111 protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
113 protected JMenuItem undoMenuItem = new JMenuItem();
115 protected JMenuItem redoMenuItem = new JMenuItem();
117 protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
119 protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
121 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
123 JMenuItem copy = new JMenuItem();
125 JMenuItem cut = new JMenuItem();
127 JMenu pasteMenu = new JMenu();
129 protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
131 protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
133 protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
135 protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
137 protected JCheckBoxMenuItem applyToAllGroups;
139 protected JMenu colourMenu = new JMenu();
141 protected JMenuItem textColour;
143 protected JCheckBoxMenuItem conservationMenuItem;
145 protected JMenuItem modifyConservation;
147 protected JCheckBoxMenuItem abovePIDThreshold;
149 protected JMenuItem modifyPID;
151 protected JMenuItem annotationColour;
153 protected JMenu sortByTreeMenu = new JMenu();
155 protected JMenu sort = new JMenu();
157 protected JMenuItem calculateTree = new JMenuItem();
159 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
161 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
163 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
165 protected JMenuItem showTranslation = new JMenuItem();
167 protected JMenuItem showReverse = new JMenuItem();
169 protected JMenuItem showReverseComplement = new JMenuItem();
171 protected JMenu showProducts = new JMenu();
173 protected JMenuItem runGroovy = new JMenuItem();
175 protected JMenuItem loadVcf;
177 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
179 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
181 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
183 protected JPanel statusPanel = new JPanel();
185 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
187 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
189 protected JMenuItem showAllAlAnnotations = new JMenuItem();
191 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
193 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
195 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
197 protected JTabbedPane tabbedPane = new JTabbedPane();
199 protected JMenuItem reload = new JMenuItem();
201 protected JMenu formatMenu = new JMenu();
203 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
205 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
207 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
209 protected JMenuItem gatherViews = new JMenuItem();
211 protected JMenuItem expandViews = new JMenuItem();
213 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
215 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
217 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
219 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
221 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
223 protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
225 protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
227 protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
229 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
231 private SequenceAnnotationOrder annotationSortOrder;
233 private boolean showAutoCalculatedAbove = false;
235 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
237 private SplitContainerI splitFrame;
244 setJMenuBar(alignFrameMenuBar);
246 // dynamically fill save as menu with available formats
247 for (String ff : FileFormats.getInstance().getWritableFormats(true))
249 JMenuItem item = new JMenuItem(ff);
251 item.addActionListener(new ActionListener()
254 public void actionPerformed(ActionEvent e)
256 outputText_actionPerformed(e);
260 outputTextboxMenu.add(item);
262 } catch (Exception e)
264 System.err.println(e.toString());
267 if (!Platform.isAMac())
269 closeMenuItem.setMnemonic('C');
270 outputTextboxMenu.setMnemonic('T');
271 undoMenuItem.setMnemonic('Z');
272 redoMenuItem.setMnemonic('0');
273 copy.setMnemonic('C');
274 cut.setMnemonic('U');
275 pasteMenu.setMnemonic('P');
276 reload.setMnemonic('R');
280 private void jbInit() throws Exception
285 JMenuItem saveAs = new JMenuItem(
286 MessageManager.getString("action.save_as"));
287 ActionListener al = new ActionListener()
290 public void actionPerformed(ActionEvent e)
292 saveAs_actionPerformed(e);
296 // FIXME getDefaultToolkit throws an exception in Headless mode
297 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
298 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
299 | KeyEvent.SHIFT_MASK,
301 addMenuActionAndAccelerator(keyStroke, saveAs, al);
303 closeMenuItem.setText(MessageManager.getString("action.close"));
304 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
305 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
306 al = new ActionListener()
309 public void actionPerformed(ActionEvent e)
311 closeMenuItem_actionPerformed(false);
314 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
316 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
317 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
318 JMenu annotationsMenu = new JMenu(
319 MessageManager.getString("action.annotations"));
320 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
321 colourMenu.setText(MessageManager.getString("action.colour"));
322 JMenu calculateMenu = new JMenu(
323 MessageManager.getString("action.calculate"));
324 webService.setText(MessageManager.getString("action.web_service"));
325 hmmerMenu.setText(MessageManager.getString("action.hmmer"));
326 hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
327 hmmerMenu.addActionListener(new ActionListener()
330 public void actionPerformed(ActionEvent e)
332 hmmerMenu_actionPerformed(e);
335 hmmerMenu.add(hmmBuild);
336 hmmerMenu.add(hmmAlign);
337 hmmerMenu.add(hmmSearch);
339 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
340 MessageManager.getString("action.select_all"));
341 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
342 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
343 al = new ActionListener()
346 public void actionPerformed(ActionEvent e)
348 selectAllSequenceMenuItem_actionPerformed(e);
351 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
353 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
354 MessageManager.getString("action.deselect_all"));
355 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
356 al = new ActionListener()
359 public void actionPerformed(ActionEvent e)
361 deselectAllSequenceMenuItem_actionPerformed(e);
364 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
366 JMenuItem invertSequenceMenuItem = new JMenuItem(
367 MessageManager.getString("action.invert_sequence_selection"));
368 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
369 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
370 al = new ActionListener()
373 public void actionPerformed(ActionEvent e)
375 invertSequenceMenuItem_actionPerformed(e);
378 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
380 JMenuItem grpsFromSelection = new JMenuItem(
381 MessageManager.getString("action.make_groups_selection"));
382 grpsFromSelection.addActionListener(new ActionListener()
385 public void actionPerformed(ActionEvent e)
387 makeGrpsFromSelection_actionPerformed(e);
390 JMenuItem expandAlignment = new JMenuItem(
391 MessageManager.getString("action.view_flanking_regions"));
392 expandAlignment.setToolTipText(
393 MessageManager.getString("label.view_flanking_regions"));
394 expandAlignment.addActionListener(new ActionListener()
397 public void actionPerformed(ActionEvent e)
402 JMenuItem remove2LeftMenuItem = new JMenuItem(
403 MessageManager.getString("action.remove_left"));
404 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
405 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
406 al = new ActionListener()
409 public void actionPerformed(ActionEvent e)
411 remove2LeftMenuItem_actionPerformed(e);
414 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
416 JMenuItem remove2RightMenuItem = new JMenuItem(
417 MessageManager.getString("action.remove_right"));
418 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
419 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
420 al = new ActionListener()
423 public void actionPerformed(ActionEvent e)
425 remove2RightMenuItem_actionPerformed(e);
428 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
430 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
431 MessageManager.getString("action.remove_empty_columns"));
432 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
433 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
434 al = new ActionListener()
437 public void actionPerformed(ActionEvent e)
439 removeGappedColumnMenuItem_actionPerformed(e);
442 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
444 JMenuItem removeAllGapsMenuItem = new JMenuItem(
445 MessageManager.getString("action.remove_all_gaps"));
446 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
447 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
448 | KeyEvent.SHIFT_MASK,
450 al = new ActionListener()
453 public void actionPerformed(ActionEvent e)
455 removeAllGapsMenuItem_actionPerformed(e);
458 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
460 JMenuItem justifyLeftMenuItem = new JMenuItem(
461 MessageManager.getString("action.left_justify_alignment"));
462 justifyLeftMenuItem.addActionListener(new ActionListener()
465 public void actionPerformed(ActionEvent e)
467 justifyLeftMenuItem_actionPerformed(e);
470 JMenuItem justifyRightMenuItem = new JMenuItem(
471 MessageManager.getString("action.right_justify_alignment"));
472 justifyRightMenuItem.addActionListener(new ActionListener()
475 public void actionPerformed(ActionEvent e)
477 justifyRightMenuItem_actionPerformed(e);
480 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
481 viewBoxesMenuItem.setState(true);
482 viewBoxesMenuItem.addActionListener(new ActionListener()
485 public void actionPerformed(ActionEvent e)
487 viewBoxesMenuItem_actionPerformed(e);
490 viewTextMenuItem.setText(MessageManager.getString("action.text"));
491 viewTextMenuItem.setState(true);
492 viewTextMenuItem.addActionListener(new ActionListener()
495 public void actionPerformed(ActionEvent e)
497 viewTextMenuItem_actionPerformed(e);
500 showNonconservedMenuItem
501 .setText(MessageManager.getString("label.show_non_conserved"));
502 showNonconservedMenuItem.setState(false);
503 showNonconservedMenuItem.addActionListener(new ActionListener()
506 public void actionPerformed(ActionEvent e)
508 showUnconservedMenuItem_actionPerformed(e);
511 JMenuItem sortPairwiseMenuItem = new JMenuItem(
512 MessageManager.getString("action.by_pairwise_id"));
513 sortPairwiseMenuItem.addActionListener(new ActionListener()
516 public void actionPerformed(ActionEvent e)
518 sortPairwiseMenuItem_actionPerformed(e);
521 JMenuItem sortIDMenuItem = new JMenuItem(
522 MessageManager.getString("action.by_id"));
523 sortIDMenuItem.addActionListener(new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 sortIDMenuItem_actionPerformed(e);
531 JMenuItem sortLengthMenuItem = new JMenuItem(
532 MessageManager.getString("action.by_length"));
533 sortLengthMenuItem.addActionListener(new ActionListener()
536 public void actionPerformed(ActionEvent e)
538 sortLengthMenuItem_actionPerformed(e);
541 JMenuItem sortGroupMenuItem = new JMenuItem(
542 MessageManager.getString("action.by_group"));
543 sortGroupMenuItem.addActionListener(new ActionListener()
546 public void actionPerformed(ActionEvent e)
548 sortGroupMenuItem_actionPerformed(e);
552 JMenuItem removeRedundancyMenuItem = new JMenuItem(
553 MessageManager.getString("action.remove_redundancy"));
554 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
555 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
556 al = new ActionListener()
559 public void actionPerformed(ActionEvent e)
561 removeRedundancyMenuItem_actionPerformed(e);
564 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
566 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
567 MessageManager.getString("action.pairwise_alignment"));
568 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
571 public void actionPerformed(ActionEvent e)
573 pairwiseAlignmentMenuItem_actionPerformed(e);
577 this.getContentPane().setLayout(new BorderLayout());
578 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
579 statusBar.setBackground(Color.white);
580 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
581 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
582 statusBar.setText(MessageManager.getString("label.status_bar"));
585 .setText(MessageManager.getString("label.out_to_textbox"));
588 annotationPanelMenuItem.setActionCommand("");
589 annotationPanelMenuItem
590 .setText(MessageManager.getString("label.show_annotations"));
591 annotationPanelMenuItem
592 .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
593 annotationPanelMenuItem.addActionListener(new ActionListener()
596 public void actionPerformed(ActionEvent e)
598 annotationPanelMenuItem_actionPerformed(e);
601 showAllAlAnnotations.setText(
602 MessageManager.getString("label.show_all_al_annotations"));
603 final boolean isAnnotationPanelShown = annotationPanelMenuItem
605 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
606 showAllAlAnnotations.addActionListener(new ActionListener()
609 public void actionPerformed(ActionEvent e)
611 showAllAnnotations_actionPerformed(false, true);
614 hideAllAlAnnotations.setText(
615 MessageManager.getString("label.hide_all_al_annotations"));
616 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
617 hideAllAlAnnotations.addActionListener(new ActionListener()
620 public void actionPerformed(ActionEvent e)
622 hideAllAnnotations_actionPerformed(false, true);
625 showAllSeqAnnotations.setText(
626 MessageManager.getString("label.show_all_seq_annotations"));
627 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
628 showAllSeqAnnotations.addActionListener(new ActionListener()
631 public void actionPerformed(ActionEvent e)
633 showAllAnnotations_actionPerformed(true, false);
636 hideAllSeqAnnotations.setText(
637 MessageManager.getString("label.hide_all_seq_annotations"));
638 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
639 hideAllSeqAnnotations.addActionListener(new ActionListener()
642 public void actionPerformed(ActionEvent e)
644 hideAllAnnotations_actionPerformed(true, false);
647 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
648 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
649 SequenceAnnotationOrder.NONE.name()));
650 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
651 MessageManager.getString("label.sort_annotations_by_sequence"));
652 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
653 MessageManager.getString("label.sort_annotations_by_label"));
656 sortAnnBySequence.setSelected(
657 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
658 sortAnnBySequence.addActionListener(new ActionListener()
661 public void actionPerformed(ActionEvent e)
663 boolean newState = sortAnnBySequence.getState();
664 sortAnnByLabel.setSelected(false);
665 setAnnotationSortOrder(
666 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
667 : SequenceAnnotationOrder.NONE);
668 sortAnnotations_actionPerformed();
671 sortAnnByLabel.setSelected(
672 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
673 sortAnnByLabel.addActionListener(new ActionListener()
676 public void actionPerformed(ActionEvent e)
678 boolean newState = sortAnnByLabel.getState();
679 sortAnnBySequence.setSelected(false);
680 setAnnotationSortOrder(
681 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
682 : SequenceAnnotationOrder.NONE);
683 sortAnnotations_actionPerformed();
686 colourTextMenuItem = new JCheckBoxMenuItem(
687 MessageManager.getString("label.colour_text"));
688 colourTextMenuItem.addActionListener(new ActionListener()
691 public void actionPerformed(ActionEvent e)
693 colourTextMenuItem_actionPerformed(e);
697 JMenuItem htmlMenuItem = new JMenuItem(
698 MessageManager.getString("label.html"));
699 htmlMenuItem.addActionListener(new ActionListener()
702 public void actionPerformed(ActionEvent e)
704 htmlMenuItem_actionPerformed(e);
708 JMenuItem createBioJS = new JMenuItem(
709 MessageManager.getString("label.biojs_html_export"));
710 createBioJS.addActionListener(new java.awt.event.ActionListener()
713 public void actionPerformed(ActionEvent e)
715 bioJSMenuItem_actionPerformed(e);
719 JMenuItem overviewMenuItem = new JMenuItem(
720 MessageManager.getString("label.overview_window"));
721 overviewMenuItem.addActionListener(new ActionListener()
724 public void actionPerformed(ActionEvent e)
726 overviewMenuItem_actionPerformed(e);
730 undoMenuItem.setEnabled(false);
731 undoMenuItem.setText(MessageManager.getString("action.undo"));
732 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
733 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
734 al = new ActionListener()
737 public void actionPerformed(ActionEvent e)
739 undoMenuItem_actionPerformed(e);
742 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
744 redoMenuItem.setEnabled(false);
745 redoMenuItem.setText(MessageManager.getString("action.redo"));
746 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
747 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
748 al = new ActionListener()
751 public void actionPerformed(ActionEvent e)
753 redoMenuItem_actionPerformed(e);
756 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
758 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
759 wrapMenuItem.addActionListener(new ActionListener()
762 public void actionPerformed(ActionEvent e)
764 wrapMenuItem_actionPerformed(e);
768 JMenuItem printMenuItem = new JMenuItem(
769 MessageManager.getString("action.print"));
770 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
771 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
772 al = new ActionListener()
775 public void actionPerformed(ActionEvent e)
777 printMenuItem_actionPerformed(e);
780 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
783 .setText(MessageManager.getString("action.show_gaps"));
784 renderGapsMenuItem.setState(true);
785 renderGapsMenuItem.addActionListener(new ActionListener()
788 public void actionPerformed(ActionEvent e)
790 renderGapsMenuItem_actionPerformed(e);
794 JMenuItem findMenuItem = new JMenuItem(
795 MessageManager.getString("action.find"));
796 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
797 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
798 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
799 MessageManager.getString("label.find_tip")));
800 al = new ActionListener()
803 public void actionPerformed(ActionEvent e)
805 findMenuItem_actionPerformed(e);
808 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
810 showSeqFeatures.setText(
811 MessageManager.getString("label.show_sequence_features"));
813 showSeqFeatures.addActionListener(new ActionListener()
816 public void actionPerformed(ActionEvent actionEvent)
818 showSeqFeatures_actionPerformed(actionEvent);
822 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
823 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
824 * void actionPerformed(ActionEvent actionEvent) {
825 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
828 .setText(MessageManager.getString("label.show_database_refs"));
829 showDbRefsMenuitem.addActionListener(new ActionListener()
833 public void actionPerformed(ActionEvent e)
835 showDbRefs_actionPerformed(e);
839 showNpFeatsMenuitem.setText(
840 MessageManager.getString("label.show_non_positional_features"));
841 showNpFeatsMenuitem.addActionListener(new ActionListener()
845 public void actionPerformed(ActionEvent e)
847 showNpFeats_actionPerformed(e);
851 showGroupConservation
852 .setText(MessageManager.getString("label.group_conservation"));
853 showGroupConservation.addActionListener(new ActionListener()
857 public void actionPerformed(ActionEvent e)
859 showGroupConservation_actionPerformed(e);
865 .setText(MessageManager.getString("label.group_consensus"));
866 showGroupConsensus.addActionListener(new ActionListener()
870 public void actionPerformed(ActionEvent e)
872 showGroupConsensus_actionPerformed(e);
876 showConsensusHistogram.setText(
877 MessageManager.getString("label.show_consensus_histogram"));
878 showConsensusHistogram.addActionListener(new ActionListener()
882 public void actionPerformed(ActionEvent e)
884 showConsensusHistogram_actionPerformed(e);
889 .setText(MessageManager.getString("label.show_consensus_logo"));
890 showSequenceLogo.addActionListener(new ActionListener()
894 public void actionPerformed(ActionEvent e)
896 showSequenceLogo_actionPerformed(e);
900 normaliseSequenceLogo
901 .setText(MessageManager.getString("label.norm_consensus_logo"));
902 normaliseSequenceLogo.addActionListener(new ActionListener()
906 public void actionPerformed(ActionEvent e)
908 normaliseSequenceLogo_actionPerformed(e);
912 applyAutoAnnotationSettings
913 .setText(MessageManager.getString("label.apply_all_groups"));
914 applyAutoAnnotationSettings.setState(false);
915 applyAutoAnnotationSettings.setVisible(true);
916 applyAutoAnnotationSettings.addActionListener(new ActionListener()
919 public void actionPerformed(ActionEvent e)
921 applyAutoAnnotationSettings_actionPerformed(e);
925 ButtonGroup buttonGroup = new ButtonGroup();
926 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
927 MessageManager.getString("label.show_first"));
928 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
929 MessageManager.getString("label.show_last"));
930 buttonGroup.add(showAutoFirst);
931 buttonGroup.add(showAutoLast);
932 final boolean autoFirst = Cache
933 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
934 showAutoFirst.setSelected(autoFirst);
935 setShowAutoCalculatedAbove(autoFirst);
936 showAutoFirst.addActionListener(new ActionListener()
939 public void actionPerformed(ActionEvent e)
941 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
942 sortAnnotations_actionPerformed();
945 showAutoLast.setSelected(!showAutoFirst.isSelected());
946 showAutoLast.addActionListener(new ActionListener()
949 public void actionPerformed(ActionEvent e)
951 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
952 sortAnnotations_actionPerformed();
956 JMenuItem deleteGroups = new JMenuItem(
957 MessageManager.getString("action.undefine_groups"));
958 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
959 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
960 al = new ActionListener()
963 public void actionPerformed(ActionEvent e)
965 deleteGroups_actionPerformed(e);
968 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
970 JMenuItem annotationColumn = new JMenuItem(
971 MessageManager.getString("action.select_by_annotation"));
972 annotationColumn.addActionListener(new ActionListener()
975 public void actionPerformed(ActionEvent e)
977 annotationColumn_actionPerformed(e);
981 JMenuItem createGroup = new JMenuItem(
982 MessageManager.getString("action.create_group"));
983 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
984 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
985 al = new ActionListener()
988 public void actionPerformed(ActionEvent e)
990 createGroup_actionPerformed(e);
993 addMenuActionAndAccelerator(keyStroke, createGroup, al);
995 JMenuItem unGroup = new JMenuItem(
996 MessageManager.getString("action.remove_group"));
997 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
998 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
999 | KeyEvent.SHIFT_MASK,
1001 al = new ActionListener()
1004 public void actionPerformed(ActionEvent e)
1006 unGroup_actionPerformed(e);
1009 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1011 copy.setText(MessageManager.getString("action.copy"));
1012 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
1013 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1015 al = new ActionListener()
1018 public void actionPerformed(ActionEvent e)
1020 copy_actionPerformed(e);
1023 addMenuActionAndAccelerator(keyStroke, copy, al);
1025 cut.setText(MessageManager.getString("action.cut"));
1026 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
1027 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1028 al = new ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 cut_actionPerformed(e);
1036 addMenuActionAndAccelerator(keyStroke, cut, al);
1038 JMenuItem delete = new JMenuItem(
1039 MessageManager.getString("action.delete"));
1040 delete.addActionListener(new ActionListener()
1043 public void actionPerformed(ActionEvent e)
1045 delete_actionPerformed(e);
1049 pasteMenu.setText(MessageManager.getString("action.paste"));
1050 JMenuItem pasteNew = new JMenuItem(
1051 MessageManager.getString("label.to_new_alignment"));
1052 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1053 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1054 | KeyEvent.SHIFT_MASK,
1056 al = new ActionListener()
1059 public void actionPerformed(ActionEvent e)
1063 pasteNew_actionPerformed(e);
1064 } catch (IOException | InterruptedException e1)
1066 // TODO Auto-generated catch block
1067 e1.printStackTrace();
1071 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1073 JMenuItem pasteThis = new JMenuItem(
1074 MessageManager.getString("label.to_this_alignment"));
1075 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
1076 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1077 al = new ActionListener()
1080 public void actionPerformed(ActionEvent e)
1084 pasteThis_actionPerformed(e);
1085 } catch (IOException | InterruptedException e1)
1087 // TODO Auto-generated catch block
1088 e1.printStackTrace();
1092 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1094 JMenuItem createPNG = new JMenuItem("PNG");
1095 createPNG.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1103 createPNG.setActionCommand(
1104 MessageManager.getString("label.save_png_image"));
1105 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1106 font.addActionListener(new ActionListener()
1109 public void actionPerformed(ActionEvent e)
1111 font_actionPerformed(e);
1115 MessageManager.getString("label.show_sequence_limits"));
1116 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1117 seqLimits.addActionListener(new ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 seqLimit_actionPerformed(e);
1125 JMenuItem epsFile = new JMenuItem("EPS");
1126 epsFile.addActionListener(new ActionListener()
1129 public void actionPerformed(ActionEvent e)
1135 JMenuItem createSVG = new JMenuItem("SVG");
1136 createSVG.addActionListener(new ActionListener()
1139 public void actionPerformed(ActionEvent e)
1145 JMenuItem loadTreeMenuItem = new JMenuItem(
1146 MessageManager.getString("label.load_associated_tree"));
1147 loadTreeMenuItem.setActionCommand(
1148 MessageManager.getString("label.load_tree_for_sequence_set"));
1149 loadTreeMenuItem.addActionListener(new ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 loadTreeMenuItem_actionPerformed(e);
1158 scaleAbove.setVisible(false);
1159 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1160 scaleAbove.addActionListener(new ActionListener()
1163 public void actionPerformed(ActionEvent e)
1165 scaleAbove_actionPerformed(e);
1168 scaleLeft.setVisible(false);
1169 scaleLeft.setSelected(true);
1170 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1171 scaleLeft.addActionListener(new ActionListener()
1174 public void actionPerformed(ActionEvent e)
1176 scaleLeft_actionPerformed(e);
1179 scaleRight.setVisible(false);
1180 scaleRight.setSelected(true);
1181 scaleRight.setText(MessageManager.getString("action.scale_right"));
1182 scaleRight.addActionListener(new ActionListener()
1185 public void actionPerformed(ActionEvent e)
1187 scaleRight_actionPerformed(e);
1190 centreColumnLabelsMenuItem.setVisible(true);
1191 centreColumnLabelsMenuItem.setState(false);
1192 centreColumnLabelsMenuItem.setText(
1193 MessageManager.getString("label.centre_column_labels"));
1194 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 centreColumnLabels_actionPerformed(e);
1202 followHighlightMenuItem.setVisible(true);
1203 followHighlightMenuItem.setState(true);
1204 followHighlightMenuItem
1205 .setText(MessageManager.getString("label.automatic_scrolling"));
1206 followHighlightMenuItem.addActionListener(new ActionListener()
1210 public void actionPerformed(ActionEvent e)
1212 followHighlight_actionPerformed();
1218 .setText(MessageManager.getString("action.by_tree_order"));
1219 sort.setText(MessageManager.getString("action.sort"));
1220 sort.addMenuListener(new MenuListener()
1223 public void menuSelected(MenuEvent e)
1225 buildTreeSortMenu();
1229 public void menuDeselected(MenuEvent e)
1234 public void menuCanceled(MenuEvent e)
1239 .setText(MessageManager.getString("label.sort_by_score"));
1240 sort.add(sortByAnnotScore);
1241 sort.addMenuListener(new javax.swing.event.MenuListener()
1245 public void menuCanceled(MenuEvent e)
1250 public void menuDeselected(MenuEvent e)
1255 public void menuSelected(MenuEvent e)
1257 buildSortByAnnotationScoresMenu();
1260 sortByAnnotScore.setVisible(false);
1263 .setText(MessageManager.getString("action.calculate_tree_pca"));
1265 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1267 .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
1268 padGapsMenuitem.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 padGapsMenuitem_actionPerformed(e);
1276 JMenuItem vamsasStore = new JMenuItem(
1277 MessageManager.getString("label.vamsas_store"));
1278 vamsasStore.setVisible(false);
1279 vamsasStore.addActionListener(new ActionListener()
1282 public void actionPerformed(ActionEvent e)
1284 vamsasStore_actionPerformed(e);
1288 .setText(MessageManager.getString("label.translate_cDNA"));
1289 showTranslation.addActionListener(new ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 showTranslation_actionPerformed(e);
1297 showReverse.setText(MessageManager.getString("label.reverse"));
1298 showReverse.addActionListener(new ActionListener()
1301 public void actionPerformed(ActionEvent e)
1303 showReverse_actionPerformed(false);
1306 showReverseComplement
1307 .setText(MessageManager.getString("label.reverse_complement"));
1308 showReverseComplement.addActionListener(new ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 showReverse_actionPerformed(true);
1317 JMenuItem extractScores = new JMenuItem(
1318 MessageManager.getString("label.extract_scores"));
1319 extractScores.addActionListener(new ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 extractScores_actionPerformed(e);
1327 extractScores.setVisible(true);
1328 // JBPNote: TODO: make gui for regex based score extraction
1330 // for show products actions see AlignFrame.canShowProducts
1331 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1333 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1334 runGroovy.setToolTipText(
1335 MessageManager.getString("label.run_groovy_tip"));
1336 runGroovy.addActionListener(new ActionListener()
1339 public void actionPerformed(ActionEvent e)
1341 runGroovy_actionPerformed();
1345 JMenuItem openFeatureSettings = new JMenuItem(
1346 MessageManager.getString("action.feature_settings"));
1347 openFeatureSettings.addActionListener(new ActionListener()
1350 public void actionPerformed(ActionEvent e)
1352 featureSettings_actionPerformed(e);
1355 JMenuItem fetchSequence = new JMenuItem(
1356 MessageManager.getString("label.fetch_sequences"));
1357 fetchSequence.addActionListener(new ActionListener()
1360 public void actionPerformed(ActionEvent e)
1362 fetchSequence_actionPerformed(e);
1366 JMenuItem associatedData = new JMenuItem(
1367 MessageManager.getString("label.load_features_annotations"));
1368 associatedData.addActionListener(new ActionListener()
1371 public void actionPerformed(ActionEvent e)
1375 associatedData_actionPerformed(e);
1376 } catch (IOException | InterruptedException e1)
1378 // TODO Auto-generated catch block
1379 e1.printStackTrace();
1383 loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
1384 loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
1385 loadVcf.addActionListener(new ActionListener()
1388 public void actionPerformed(ActionEvent e)
1390 loadVcf_actionPerformed();
1393 autoCalculate.setText(
1394 MessageManager.getString("label.autocalculate_consensus"));
1395 autoCalculate.setState(
1396 jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
1397 autoCalculate.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 autoCalculate_actionPerformed(e);
1406 MessageManager.getString("label.sort_alignment_new_tree"));
1407 sortByTree.setToolTipText("<html>" + MessageManager.getString(
1408 "label.enable_automatically_sort_alignment_when_open_new_tree"));
1410 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1411 sortByTree.addActionListener(new ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 sortByTreeOption_actionPerformed(e);
1420 listenToViewSelections.setText(
1421 MessageManager.getString("label.listen_for_selections"));
1422 listenToViewSelections
1423 .setToolTipText("<html>" + MessageManager.getString(
1424 "label.selections_mirror_selections_made_same_sequences_other_views"));
1425 listenToViewSelections.setState(false);
1426 listenToViewSelections.addActionListener(new ActionListener()
1429 public void actionPerformed(ActionEvent e)
1431 listenToViewSelections_actionPerformed(e);
1435 JMenu addSequenceMenu = new JMenu(
1436 MessageManager.getString("label.add_sequences"));
1437 JMenuItem addFromFile = new JMenuItem(
1438 MessageManager.getString("label.from_file"));
1439 addFromFile.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent e)
1444 addFromFile_actionPerformed(e);
1447 JMenuItem addFromText = new JMenuItem(
1448 MessageManager.getString("label.from_textbox"));
1449 addFromText.addActionListener(new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 addFromText_actionPerformed(e);
1457 JMenuItem addFromURL = new JMenuItem(
1458 MessageManager.getString("label.from_url"));
1459 addFromURL.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 addFromURL_actionPerformed(e);
1467 JMenuItem exportFeatures = new JMenuItem(
1468 MessageManager.getString("label.export_features"));
1469 exportFeatures.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 exportFeatures_actionPerformed(e);
1477 JMenuItem exportAnnotations = new JMenuItem(
1478 MessageManager.getString("label.export_annotations"));
1479 exportAnnotations.addActionListener(new ActionListener()
1482 public void actionPerformed(ActionEvent e)
1484 exportAnnotations_actionPerformed(e);
1487 statusPanel.setLayout(new GridLayout());
1488 JMenuItem showAllSeqs = new JMenuItem(
1489 MessageManager.getString("label.all_sequences"));
1490 showAllSeqs.setToolTipText(
1491 MessageManager.getString("label.toggle_sequence_visibility"));
1492 showAllSeqs.addActionListener(new ActionListener()
1495 public void actionPerformed(ActionEvent e)
1497 showAllSeqs_actionPerformed(e);
1500 JMenuItem showAllColumns = new JMenuItem(
1501 MessageManager.getString("label.all_columns"));
1502 showAllColumns.setToolTipText(
1503 MessageManager.getString("label.toggle_columns_visibility"));
1504 showAllColumns.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 showAllColumns_actionPerformed(e);
1512 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1513 JMenuItem hideSelSequences = new JMenuItem(
1514 MessageManager.getString("label.selected_sequences"));
1515 hideSelSequences.setToolTipText(
1516 MessageManager.getString("label.toggle_sequence_visibility"));
1517 hideSelSequences.addActionListener(new ActionListener()
1520 public void actionPerformed(ActionEvent e)
1522 hideSelSequences_actionPerformed(e);
1525 JMenuItem hideSelColumns = new JMenuItem(
1526 MessageManager.getString("label.selected_columns"));
1527 hideSelColumns.setToolTipText(
1528 MessageManager.getString("label.toggle_columns_visibility"));
1529 hideSelColumns.addActionListener(new ActionListener()
1532 public void actionPerformed(ActionEvent e)
1534 hideSelColumns_actionPerformed(e);
1537 JMenuItem hideAllSelection = new JMenuItem(
1538 MessageManager.getString("label.selected_region"));
1539 hideAllSelection.addActionListener(new ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 hideAllSelection_actionPerformed(e);
1547 // TODO: should be hidden if no selection exists.
1548 JMenuItem hideAllButSelection = new JMenuItem(
1549 MessageManager.getString("label.all_but_selected_region"));
1550 hideAllButSelection.addActionListener(new ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 hideAllButSelection_actionPerformed(e);
1558 JMenuItem showAllhidden = new JMenuItem(
1559 MessageManager.getString("label.all_sequences_columns"));
1560 showAllhidden.setToolTipText(MessageManager
1561 .getString("label.toggles_visibility_hidden_selected_regions"));
1562 showAllhidden.addActionListener(new ActionListener()
1565 public void actionPerformed(ActionEvent e)
1567 showAllhidden_actionPerformed(e);
1570 hiddenMarkers.setText(
1571 MessageManager.getString("action.show_hidden_markers"));
1572 hiddenMarkers.addActionListener(new ActionListener()
1575 public void actionPerformed(ActionEvent e)
1577 hiddenMarkers_actionPerformed(e);
1581 JMenuItem invertColSel = new JMenuItem(
1582 MessageManager.getString("action.invert_column_selection"));
1583 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1584 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1585 | KeyEvent.ALT_MASK,
1587 al = new ActionListener()
1590 public void actionPerformed(ActionEvent e)
1592 invertColSel_actionPerformed(e);
1595 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1597 showComplementMenuItem.setVisible(false);
1598 showComplementMenuItem.addActionListener(new ActionListener()
1601 public void actionPerformed(ActionEvent e)
1603 showComplement_actionPerformed(showComplementMenuItem.getState());
1607 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1610 public void stateChanged(ChangeEvent evt)
1612 JTabbedPane pane = (JTabbedPane) evt.getSource();
1613 int sel = pane.getSelectedIndex();
1614 tabSelectionChanged(sel);
1617 tabbedPane.addMouseListener(new MouseAdapter()
1620 public void mousePressed(MouseEvent e)
1622 if (e.isPopupTrigger()) // Mac
1624 tabbedPane_mousePressed(e);
1629 public void mouseReleased(MouseEvent e)
1631 if (e.isPopupTrigger()) // Windows
1633 tabbedPane_mousePressed(e);
1637 tabbedPane.addFocusListener(new FocusAdapter()
1640 public void focusGained(FocusEvent e)
1642 tabbedPane_focusGained(e);
1646 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
1647 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
1648 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1649 al = new ActionListener()
1652 public void actionPerformed(ActionEvent e)
1654 save_actionPerformed(e);
1657 addMenuActionAndAccelerator(keyStroke, save, al);
1659 reload.setEnabled(false);
1660 reload.setText(MessageManager.getString("action.reload"));
1661 reload.addActionListener(new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 reload_actionPerformed(e);
1670 JMenuItem newView = new JMenuItem(
1671 MessageManager.getString("action.new_view"));
1672 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
1673 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
1674 al = new ActionListener()
1677 public void actionPerformed(ActionEvent e)
1679 newView_actionPerformed(e);
1682 addMenuActionAndAccelerator(keyStroke, newView, al);
1684 tabbedPane.setToolTipText("<html><i>"
1685 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1688 formatMenu.setText(MessageManager.getString("action.format"));
1689 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
1691 idRightAlign.setText(
1692 MessageManager.getString("label.right_align_sequence_id"));
1693 idRightAlign.addActionListener(new ActionListener()
1696 public void actionPerformed(ActionEvent e)
1698 idRightAlign_actionPerformed(e);
1702 gatherViews.setEnabled(false);
1703 gatherViews.setText(MessageManager.getString("action.gather_views"));
1704 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
1705 al = new ActionListener()
1708 public void actionPerformed(ActionEvent e)
1710 gatherViews_actionPerformed(e);
1713 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
1715 expandViews.setEnabled(false);
1716 expandViews.setText(MessageManager.getString("action.expand_views"));
1717 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
1718 al = new ActionListener()
1721 public void actionPerformed(ActionEvent e)
1723 expandViews_actionPerformed(e);
1726 addMenuActionAndAccelerator(keyStroke, expandViews, al);
1728 JMenuItem pageSetup = new JMenuItem(
1729 MessageManager.getString("action.page_setup"));
1730 pageSetup.addActionListener(new ActionListener()
1733 public void actionPerformed(ActionEvent e)
1735 pageSetup_actionPerformed(e);
1738 JMenuItem alignmentProperties = new JMenuItem(
1739 MessageManager.getString("label.alignment_props"));
1740 alignmentProperties.addActionListener(new ActionListener()
1743 public void actionPerformed(ActionEvent actionEvent)
1745 alignmentProperties();
1748 JMenuItem selectHighlighted = new JMenuItem(
1749 MessageManager.getString("action.select_highlighted_columns"));
1750 selectHighlighted.setToolTipText(
1751 MessageManager.getString("tooltip.select_highlighted_columns"));
1752 al = new ActionListener()
1755 public void actionPerformed(ActionEvent actionEvent)
1757 selectHighlightedColumns_actionPerformed(actionEvent);
1760 hmmBuildRun.setText(MessageManager.formatMessage(
1761 "label.action_with_default_settings", "hmmbuild"));
1762 hmmBuildRun.addActionListener(new ActionListener()
1765 public void actionPerformed(ActionEvent e)
1767 hmmBuild_actionPerformed(true);
1770 hmmBuildSettings.setText(
1771 MessageManager.getString("label.edit_settings_and_run"));
1772 hmmBuildSettings.addActionListener(new ActionListener()
1775 public void actionPerformed(ActionEvent e)
1777 hmmBuild_actionPerformed(false);
1780 hmmAlignRun.setText(MessageManager.formatMessage(
1781 "label.action_with_default_settings", "hmmalign"));
1782 hmmAlignRun.addActionListener(new ActionListener()
1785 public void actionPerformed(ActionEvent e)
1787 hmmAlign_actionPerformed(true);
1790 hmmAlignSettings.setText(
1791 MessageManager.getString("label.edit_settings_and_run"));
1792 hmmAlignSettings.addActionListener(new ActionListener()
1795 public void actionPerformed(ActionEvent e)
1797 hmmAlign_actionPerformed(false);
1800 hmmSearchRun.setText(MessageManager.formatMessage(
1801 "label.action_with_default_settings", "hmmsearch"));
1802 hmmSearchRun.addActionListener(new ActionListener()
1805 public void actionPerformed(ActionEvent e)
1807 hmmSearch_actionPerformed(true);
1810 hmmSearchSettings.setText(
1811 MessageManager.getString("label.edit_settings_and_run"));
1812 hmmSearchSettings.addActionListener(new ActionListener()
1815 public void actionPerformed(ActionEvent e)
1817 hmmSearch_actionPerformed(false);
1820 addDatabase.setText(MessageManager.getString("label.add_database"));
1821 addDatabase.addActionListener(new ActionListener()
1824 public void actionPerformed(ActionEvent e)
1828 addDatabase_actionPerformed();
1829 } catch (IOException e1)
1831 e1.printStackTrace();
1835 selectHighlighted.addActionListener(al);
1836 JMenu tooltipSettingsMenu = new JMenu(
1837 MessageManager.getString("label.sequence_id_tooltip"));
1838 JMenu autoAnnMenu = new JMenu(
1839 MessageManager.getString("label.autocalculated_annotation"));
1841 JMenu exportImageMenu = new JMenu(
1842 MessageManager.getString("label.export_image"));
1843 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
1844 alignFrameMenuBar.add(fileMenu);
1845 alignFrameMenuBar.add(editMenu);
1846 alignFrameMenuBar.add(selectMenu);
1847 alignFrameMenuBar.add(viewMenu);
1848 alignFrameMenuBar.add(annotationsMenu);
1849 alignFrameMenuBar.add(formatMenu);
1850 alignFrameMenuBar.add(colourMenu);
1851 alignFrameMenuBar.add(calculateMenu);
1852 alignFrameMenuBar.add(webService);
1853 alignFrameMenuBar.add(hmmerMenu);
1855 fileMenu.add(fetchSequence);
1856 fileMenu.add(addSequenceMenu);
1857 fileMenu.add(reload);
1858 fileMenu.addSeparator();
1859 fileMenu.add(vamsasStore);
1861 fileMenu.add(saveAs);
1862 fileMenu.add(outputTextboxMenu);
1863 fileMenu.add(pageSetup);
1864 fileMenu.add(printMenuItem);
1865 fileMenu.addSeparator();
1866 fileMenu.add(exportImageMenu);
1867 fileMenu.add(exportFeatures);
1868 fileMenu.add(exportAnnotations);
1869 fileMenu.add(loadTreeMenuItem);
1870 fileMenu.add(associatedData);
1871 fileMenu.add(loadVcf);
1872 fileMenu.addSeparator();
1873 fileMenu.add(closeMenuItem);
1875 pasteMenu.add(pasteNew);
1876 pasteMenu.add(pasteThis);
1877 editMenu.add(undoMenuItem);
1878 editMenu.add(redoMenuItem);
1881 editMenu.add(pasteMenu);
1882 editMenu.add(delete);
1883 editMenu.addSeparator();
1884 editMenu.add(remove2LeftMenuItem);
1885 editMenu.add(remove2RightMenuItem);
1886 editMenu.add(removeGappedColumnMenuItem);
1887 editMenu.add(removeAllGapsMenuItem);
1888 editMenu.add(removeRedundancyMenuItem);
1889 editMenu.addSeparator();
1890 // dont add these yet in the CVS build - they cannot be undone!
1891 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1892 // editMenu.add(justifyLeftMenuItem);
1893 // editMenu.add(justifyRightMenuItem);
1894 // editMenu.addSeparator();
1895 editMenu.add(padGapsMenuitem);
1897 showMenu.add(showAllColumns);
1898 showMenu.add(showAllSeqs);
1899 showMenu.add(showAllhidden);
1900 hideMenu.add(hideSelColumns);
1901 hideMenu.add(hideSelSequences);
1902 hideMenu.add(hideAllSelection);
1903 hideMenu.add(hideAllButSelection);
1904 viewMenu.add(newView);
1905 viewMenu.add(expandViews);
1906 viewMenu.add(gatherViews);
1907 viewMenu.addSeparator();
1908 viewMenu.add(showMenu);
1909 viewMenu.add(hideMenu);
1910 viewMenu.add(showComplementMenuItem);
1911 viewMenu.addSeparator();
1912 viewMenu.add(followHighlightMenuItem);
1913 viewMenu.addSeparator();
1914 viewMenu.add(showSeqFeatures);
1915 // viewMenu.add(showSeqFeaturesHeight);
1916 viewMenu.add(openFeatureSettings);
1917 tooltipSettingsMenu.add(showDbRefsMenuitem);
1918 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1919 viewMenu.add(tooltipSettingsMenu);
1920 viewMenu.addSeparator();
1921 viewMenu.add(alignmentProperties);
1922 viewMenu.addSeparator();
1923 viewMenu.add(overviewMenuItem);
1925 annotationsMenu.add(annotationPanelMenuItem);
1926 annotationsMenu.addSeparator();
1927 annotationsMenu.add(showAllAlAnnotations);
1928 annotationsMenu.add(hideAllAlAnnotations);
1929 annotationsMenu.addSeparator();
1930 annotationsMenu.add(showAllSeqAnnotations);
1931 annotationsMenu.add(hideAllSeqAnnotations);
1932 annotationsMenu.add(sortAnnBySequence);
1933 annotationsMenu.add(sortAnnByLabel);
1934 annotationsMenu.addSeparator();
1935 autoAnnMenu.add(showAutoFirst);
1936 autoAnnMenu.add(showAutoLast);
1937 autoAnnMenu.addSeparator();
1938 autoAnnMenu.add(applyAutoAnnotationSettings);
1939 autoAnnMenu.add(showConsensusHistogram);
1940 autoAnnMenu.add(showSequenceLogo);
1941 autoAnnMenu.add(normaliseSequenceLogo);
1942 autoAnnMenu.addSeparator();
1943 autoAnnMenu.add(showGroupConservation);
1944 autoAnnMenu.add(showGroupConsensus);
1945 annotationsMenu.add(autoAnnMenu);
1947 sort.add(sortIDMenuItem);
1948 sort.add(sortLengthMenuItem);
1949 sort.add(sortGroupMenuItem);
1950 sort.add(sortPairwiseMenuItem);
1951 sort.add(sortByTreeMenu);
1952 calculateMenu.add(sort);
1953 calculateMenu.add(calculateTree);
1954 calculateMenu.addSeparator();
1955 calculateMenu.add(pairwiseAlignmentMenuItem);
1956 calculateMenu.addSeparator();
1957 calculateMenu.add(showTranslation);
1958 calculateMenu.add(showReverse);
1959 calculateMenu.add(showReverseComplement);
1960 calculateMenu.add(showProducts);
1961 calculateMenu.add(autoCalculate);
1962 calculateMenu.add(sortByTree);
1963 calculateMenu.addSeparator();
1964 calculateMenu.add(expandAlignment);
1965 calculateMenu.add(extractScores);
1966 calculateMenu.addSeparator();
1967 calculateMenu.add(runGroovy);
1969 webServiceNoServices = new JMenuItem(
1970 MessageManager.getString("label.no_services"));
1971 webService.add(webServiceNoServices);
1972 exportImageMenu.add(htmlMenuItem);
1973 exportImageMenu.add(epsFile);
1974 exportImageMenu.add(createPNG);
1975 exportImageMenu.add(createBioJS);
1976 exportImageMenu.add(createSVG);
1977 addSequenceMenu.add(addFromFile);
1978 addSequenceMenu.add(addFromText);
1979 addSequenceMenu.add(addFromURL);
1980 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1981 statusPanel.add(statusBar, null);
1982 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1984 formatMenu.add(font);
1985 formatMenu.addSeparator();
1986 formatMenu.add(wrapMenuItem);
1987 formatMenu.add(scaleAbove);
1988 formatMenu.add(scaleLeft);
1989 formatMenu.add(scaleRight);
1990 formatMenu.add(seqLimits);
1991 formatMenu.add(idRightAlign);
1992 formatMenu.add(hiddenMarkers);
1993 formatMenu.add(viewBoxesMenuItem);
1994 formatMenu.add(viewTextMenuItem);
1995 formatMenu.add(colourTextMenuItem);
1996 formatMenu.add(renderGapsMenuItem);
1997 formatMenu.add(centreColumnLabelsMenuItem);
1998 formatMenu.add(showNonconservedMenuItem);
1999 selectMenu.add(findMenuItem);
2000 selectMenu.addSeparator();
2001 selectMenu.add(selectAllSequenceMenuItem);
2002 selectMenu.add(deselectAllSequenceMenuItem);
2003 selectMenu.add(invertSequenceMenuItem);
2004 selectMenu.add(invertColSel);
2005 selectMenu.add(createGroup);
2006 selectMenu.add(unGroup);
2007 selectMenu.add(grpsFromSelection);
2008 selectMenu.add(deleteGroups);
2009 selectMenu.add(annotationColumn);
2010 selectMenu.add(selectHighlighted);
2011 // TODO - determine if the listenToViewSelections button is needed : see bug
2013 // selectMenu.addSeparator();
2014 // selectMenu.add(listenToViewSelections);
2017 public void hmmerMenu_actionPerformed(ActionEvent e)
2023 * Constructs the entries on the HMMER menu (does not add them to the menu).
2025 protected void initHMMERMenu()
2027 hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
2028 hmmAlignSettings = new JMenuItem(
2029 MessageManager.getString("label.edit_settings_and_run"));
2030 hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
2031 "label.action_with_default_settings", "hmmalign"));
2032 hmmAlign.add(hmmAlignSettings);
2033 hmmAlign.add(hmmAlignRun);
2034 hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
2035 hmmBuildSettings = new JMenuItem(
2036 MessageManager.getString("label.edit_settings_and_run"));
2037 hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
2038 "label.action_with_default_settings", "hmmbuild"));
2039 hmmBuild.add(hmmBuildSettings);
2040 hmmBuild.add(hmmBuildRun);
2041 hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
2042 hmmSearchSettings = new JMenuItem(
2043 MessageManager.getString("label.edit_settings_and_run"));
2044 hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
2045 "label.action_with_default_settings", "hmmsearch"));
2046 addDatabase = new JMenuItem(
2047 MessageManager.getString("label.add_database"));
2048 hmmSearch.add(hmmSearchSettings);
2049 hmmSearch.add(hmmSearchRun);
2050 hmmSearch.add(addDatabase);
2053 protected void loadVcf_actionPerformed()
2058 * Constructs the entries on the Colour menu (but does not add them to the
2061 protected void initColourMenu()
2063 applyToAllGroups = new JCheckBoxMenuItem(
2064 MessageManager.getString("label.apply_colour_to_all_groups"));
2065 applyToAllGroups.addActionListener(new ActionListener()
2068 public void actionPerformed(ActionEvent e)
2070 applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
2074 textColour = new JMenuItem(
2075 MessageManager.getString("label.text_colour"));
2076 textColour.addActionListener(new ActionListener()
2079 public void actionPerformed(ActionEvent e)
2081 textColour_actionPerformed();
2085 conservationMenuItem = new JCheckBoxMenuItem(
2086 MessageManager.getString("action.by_conservation"));
2087 conservationMenuItem.addActionListener(new ActionListener()
2090 public void actionPerformed(ActionEvent e)
2092 conservationMenuItem_actionPerformed(
2093 conservationMenuItem.isSelected());
2097 abovePIDThreshold = new JCheckBoxMenuItem(
2098 MessageManager.getString("label.above_identity_threshold"));
2099 abovePIDThreshold.addActionListener(new ActionListener()
2102 public void actionPerformed(ActionEvent e)
2104 abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
2107 modifyPID = new JMenuItem(
2108 MessageManager.getString("label.modify_identity_threshold"));
2109 modifyPID.addActionListener(new ActionListener()
2112 public void actionPerformed(ActionEvent e)
2114 modifyPID_actionPerformed();
2117 modifyConservation = new JMenuItem(MessageManager
2118 .getString("label.modify_conservation_threshold"));
2119 modifyConservation.addActionListener(new ActionListener()
2122 public void actionPerformed(ActionEvent e)
2124 modifyConservation_actionPerformed();
2128 annotationColour = new JMenuItem(
2129 MessageManager.getString("action.by_annotation"));
2130 annotationColour.addActionListener(new ActionListener()
2133 public void actionPerformed(ActionEvent e)
2135 annotationColour_actionPerformed();
2140 protected void selectHighlightedColumns_actionPerformed(
2141 ActionEvent actionEvent)
2143 // TODO Auto-generated method stub
2148 * Generate the reverse sequence (or reverse complement if the flag is true)
2149 * and add it to the alignment
2153 protected void showReverse_actionPerformed(boolean complement)
2158 * Try to run script in a Groovy console, having first ensured that this
2159 * alignframe is set as currentAlignFrame in Desktop
2161 protected void runGroovy_actionPerformed()
2167 * Adds the given action listener and key accelerator to the given menu item.
2168 * Also saves in a lookup table to support lookup of action by key stroke.
2172 * @param actionListener
2174 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2175 JMenuItem menuItem, ActionListener actionListener)
2177 menuItem.setAccelerator(keyStroke);
2178 accelerators.put(keyStroke, menuItem);
2179 menuItem.addActionListener(actionListener);
2183 * Action on clicking sort annotations by type.
2187 protected void sortAnnotations_actionPerformed()
2192 * Action on clicking Show all annotations.
2194 * @param forSequences
2195 * update sequence-related annotations
2196 * @param forAlignment
2197 * update non-sequence-related annotations
2199 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2200 boolean forAlignment)
2202 setAnnotationsVisibility(true, forSequences, forAlignment);
2206 * Action on clicking Hide all annotations.
2208 * @param forSequences
2209 * update sequence-related annotations
2210 * @param forAlignment
2211 * update non-sequence-related annotations
2213 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2214 boolean forAlignment)
2216 setAnnotationsVisibility(false, forSequences, forAlignment);
2220 * Set the visibility of annotations to true or false. Can act on
2221 * sequence-related annotations, or alignment-related, or both.
2224 * @param forSequences
2225 * update sequence-related annotations
2226 * @param forAlignment
2227 * update non-sequence-related annotations
2229 protected void setAnnotationsVisibility(boolean visible,
2230 boolean forSequences, boolean forAlignment)
2235 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2237 // TODO Auto-generated method stub
2241 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2243 // TODO Auto-generated method stub
2247 protected void showAllhidden_actionPerformed(ActionEvent e)
2249 // TODO Auto-generated method stub
2253 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2255 // TODO Auto-generated method stub
2259 protected void hideAllSelection_actionPerformed(ActionEvent e)
2261 // TODO Auto-generated method stub
2265 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2267 // TODO Auto-generated method stub
2271 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2273 // TODO Auto-generated method stub
2277 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2279 // TODO Auto-generated method stub
2283 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2285 // TODO Auto-generated method stub
2289 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2291 // TODO Auto-generated method stub
2295 protected void showGroupConservation_actionPerformed(ActionEvent e)
2297 // TODO Auto-generated method stub
2301 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2303 // TODO Auto-generated method stub
2307 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2309 // TODO Auto-generated method stub
2313 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2315 // TODO Auto-generated method stub
2319 protected void followHighlight_actionPerformed()
2321 // TODO Auto-generated method stub
2325 protected void showNpFeats_actionPerformed(ActionEvent e)
2327 // TODO Auto-generated method stub
2331 protected void showDbRefs_actionPerformed(ActionEvent e)
2333 // TODO Auto-generated method stub
2337 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2341 protected void buildSortByAnnotationScoresMenu()
2345 protected void extractScores_actionPerformed(ActionEvent e)
2349 protected void outputText_actionPerformed(ActionEvent e)
2353 public void addFromFile_actionPerformed(ActionEvent e)
2358 public void addFromText_actionPerformed(ActionEvent e)
2363 public void addFromURL_actionPerformed(ActionEvent e)
2368 public void exportFeatures_actionPerformed(ActionEvent e)
2373 public void exportAnnotations_actionPerformed(ActionEvent e)
2378 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2382 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2387 protected void closeMenuItem_actionPerformed(boolean b)
2391 protected void redoMenuItem_actionPerformed(ActionEvent e)
2395 protected void undoMenuItem_actionPerformed(ActionEvent e)
2399 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2403 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2407 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2411 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2415 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2419 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2423 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2427 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2431 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2435 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2439 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2443 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2447 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2451 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2455 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2459 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2463 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2467 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2471 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2475 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2479 protected void conservationMenuItem_actionPerformed(boolean selected)
2483 protected void printMenuItem_actionPerformed(ActionEvent e)
2487 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2491 protected void findMenuItem_actionPerformed(ActionEvent e)
2495 protected void abovePIDThreshold_actionPerformed(boolean selected)
2499 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2503 protected void deleteGroups_actionPerformed(ActionEvent e)
2507 protected void createGroup_actionPerformed(ActionEvent e)
2511 protected void unGroup_actionPerformed(ActionEvent e)
2515 protected void copy_actionPerformed(ActionEvent e)
2519 protected void cut_actionPerformed(ActionEvent e)
2523 protected void delete_actionPerformed(ActionEvent e)
2527 protected void pasteNew_actionPerformed(ActionEvent e)
2528 throws IOException, InterruptedException
2532 protected void pasteThis_actionPerformed(ActionEvent e)
2533 throws IOException, InterruptedException
2537 protected void applyToAllGroups_actionPerformed(boolean selected)
2541 protected void hmmBuild_actionPerformed(boolean withDefaults)
2545 protected void hmmSearch_actionPerformed(boolean withDefaults)
2549 protected void addDatabase_actionPerformed()
2550 throws FileFormatException, IOException
2554 protected void hmmAlign_actionPerformed(boolean withDefaults)
2558 public void createPNG(java.io.File f)
2562 protected void font_actionPerformed(ActionEvent e)
2566 protected void seqLimit_actionPerformed(ActionEvent e)
2570 public void seqDBRef_actionPerformed(ActionEvent e)
2575 public void createEPS(java.io.File f)
2579 public void createSVG(java.io.File f)
2584 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2590 * Template method to handle the 'load T-Coffee scores' menu event.
2592 * Subclasses override this method to provide a custom action.
2597 protected void loadScores_actionPerformed(ActionEvent event)
2602 protected void jpred_actionPerformed(ActionEvent e)
2606 protected void scaleAbove_actionPerformed(ActionEvent e)
2610 protected void scaleLeft_actionPerformed(ActionEvent e)
2614 protected void scaleRight_actionPerformed(ActionEvent e)
2618 protected void modifyPID_actionPerformed()
2622 protected void modifyConservation_actionPerformed()
2626 protected void saveAs_actionPerformed(ActionEvent e)
2630 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2634 public void vamsasStore_actionPerformed(ActionEvent e)
2639 public void vamsasLoad_actionPerformed(ActionEvent e)
2644 public void showTranslation_actionPerformed(ActionEvent e)
2649 public void featureSettings_actionPerformed(ActionEvent e)
2654 public void fetchSequence_actionPerformed(ActionEvent e)
2659 public void smoothFont_actionPerformed(ActionEvent e)
2664 public void annotationColour_actionPerformed()
2668 public void annotationColumn_actionPerformed(ActionEvent e)
2672 public void associatedData_actionPerformed(ActionEvent e)
2673 throws IOException, InterruptedException
2678 public void autoCalculate_actionPerformed(ActionEvent e)
2683 public void sortByTreeOption_actionPerformed(ActionEvent e)
2688 public void showAllSeqs_actionPerformed(ActionEvent e)
2693 public void showAllColumns_actionPerformed(ActionEvent e)
2698 public void hideSelSequences_actionPerformed(ActionEvent e)
2703 public void hideSelColumns_actionPerformed(ActionEvent e)
2708 public void hiddenMarkers_actionPerformed(ActionEvent e)
2713 public void findPdbId_actionPerformed(ActionEvent e)
2718 public void enterPdbId_actionPerformed(ActionEvent e)
2723 public void pdbFile_actionPerformed(ActionEvent e)
2728 public void invertColSel_actionPerformed(ActionEvent e)
2733 public void tabSelectionChanged(int sel)
2738 public void tabbedPane_mousePressed(MouseEvent e)
2743 public void tabbedPane_focusGained(FocusEvent e)
2748 public void save_actionPerformed(ActionEvent e)
2753 public void reload_actionPerformed(ActionEvent e)
2758 public void newView_actionPerformed(ActionEvent e)
2763 public void textColour_actionPerformed()
2768 public void idRightAlign_actionPerformed(ActionEvent e)
2773 public void expandViews_actionPerformed(ActionEvent e)
2778 public void gatherViews_actionPerformed(ActionEvent e)
2783 public void buildTreeSortMenu()
2788 public void pageSetup_actionPerformed(ActionEvent e)
2793 public void alignmentProperties()
2798 protected void expand_newalign(ActionEvent e)
2800 // TODO Auto-generated method stub
2804 protected boolean isShowAutoCalculatedAbove()
2806 return showAutoCalculatedAbove;
2809 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
2811 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
2814 protected SequenceAnnotationOrder getAnnotationSortOrder()
2816 return annotationSortOrder;
2819 protected void setAnnotationSortOrder(
2820 SequenceAnnotationOrder annotationSortOrder)
2822 this.annotationSortOrder = annotationSortOrder;
2825 public Map<KeyStroke, JMenuItem> getAccelerators()
2827 return this.accelerators;
2831 * Returns the selected index of the tabbed pane, or -1 if none selected
2832 * (including the case where the tabbed pane has not been made visible).
2836 public int getTabIndex()
2838 return tabbedPane.getSelectedIndex();
2841 public JPanel getStatusPanel()
2847 * Sets a reference to the containing split frame. Also makes the 'toggle
2848 * split view' menu item visible and checked.
2852 public void setSplitFrame(SplitContainerI sf)
2854 this.splitFrame = sf;
2857 this.showComplementMenuItem.setVisible(true);
2858 this.showComplementMenuItem.setState(true);
2862 public SplitContainerI getSplitViewContainer()
2864 return this.splitFrame;
2867 protected void showComplement_actionPerformed(boolean complement)