2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.api.SplitContainerI;
25 import jalview.bin.Cache;
26 import jalview.gui.JvSwingUtils;
27 import jalview.gui.Preferences;
28 import jalview.io.FileFormat;
29 import jalview.schemes.ColourSchemeProperty;
30 import jalview.util.MessageManager;
32 import java.awt.BorderLayout;
33 import java.awt.Color;
34 import java.awt.GridLayout;
35 import java.awt.Toolkit;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.FocusAdapter;
39 import java.awt.event.FocusEvent;
40 import java.awt.event.KeyEvent;
41 import java.awt.event.MouseAdapter;
42 import java.awt.event.MouseEvent;
43 import java.util.HashMap;
46 import javax.swing.BorderFactory;
47 import javax.swing.ButtonGroup;
48 import javax.swing.JCheckBoxMenuItem;
49 import javax.swing.JInternalFrame;
50 import javax.swing.JLabel;
51 import javax.swing.JMenu;
52 import javax.swing.JMenuBar;
53 import javax.swing.JMenuItem;
54 import javax.swing.JOptionPane;
55 import javax.swing.JPanel;
56 import javax.swing.JRadioButtonMenuItem;
57 import javax.swing.JTabbedPane;
58 import javax.swing.KeyStroke;
59 import javax.swing.event.ChangeEvent;
60 import javax.swing.event.MenuEvent;
61 import javax.swing.event.MenuListener;
63 public class GAlignFrame extends JInternalFrame
65 protected JMenuBar alignFrameMenuBar = new JMenuBar();
67 protected JMenuItem closeMenuItem = new JMenuItem();
69 protected JMenu colourMenu = new JMenu();
71 protected JMenu webService = new JMenu();
73 protected JMenuItem webServiceNoServices;
75 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
77 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
79 protected JMenu sortByAnnotScore = new JMenu();
81 public JLabel statusBar = new JLabel();
83 protected JMenu outputTextboxMenu = new JMenu();
85 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
87 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
89 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
91 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
93 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
95 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
113 // protected JRadioButtonMenuItem covariationColour = new
114 // JRadioButtonMenuItem();
116 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
118 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
120 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
122 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
124 protected JMenuItem undoMenuItem = new JMenuItem();
126 protected JMenuItem redoMenuItem = new JMenuItem();
128 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
130 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
132 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
134 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
136 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
138 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
140 JMenuItem copy = new JMenuItem();
142 JMenuItem cut = new JMenuItem();
144 JMenu pasteMenu = new JMenu();
146 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
148 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
152 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
154 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
156 protected JMenuItem modifyConservation = new JMenuItem();
158 protected JMenu sortByTreeMenu = new JMenu();
160 protected JMenu sort = new JMenu();
162 protected JMenu calculateTree = new JMenu();
164 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
166 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
168 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
170 protected ButtonGroup colours = new ButtonGroup();
172 protected JMenuItem showTranslation = new JMenuItem();
174 protected JMenuItem showReverse = new JMenuItem();
176 protected JMenuItem showReverseComplement = new JMenuItem();
178 protected JMenu showProducts = new JMenu();
180 protected JMenuItem runGroovy = new JMenuItem();
182 protected JMenuItem rnahelicesColour = new JMenuItem();
184 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
186 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
188 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
190 protected JPanel statusPanel = new JPanel();
192 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
194 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
196 protected JMenuItem showAllAlAnnotations = new JMenuItem();
198 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
200 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
202 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
204 protected JTabbedPane tabbedPane = new JTabbedPane();
206 protected JMenuItem reload = new JMenuItem();
208 protected JMenu formatMenu = new JMenu();
210 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
212 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
214 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
216 protected JMenuItem gatherViews = new JMenuItem();
218 protected JMenuItem expandViews = new JMenuItem();
220 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
222 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
224 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
226 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
228 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
230 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
232 private SequenceAnnotationOrder annotationSortOrder;
234 private boolean showAutoCalculatedAbove = false;
236 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
238 private SplitContainerI splitFrame;
245 setJMenuBar(alignFrameMenuBar);
247 // dynamically fill save as menu with available formats
248 for (String ff : FileFormat.getWritableFormats(true))
250 JMenuItem item = new JMenuItem(ff);
252 item.addActionListener(new ActionListener()
255 public void actionPerformed(ActionEvent e)
257 outputText_actionPerformed(e);
261 outputTextboxMenu.add(item);
263 } catch (Exception e)
265 System.err.println(e.toString());
268 if (!jalview.util.Platform.isAMac())
270 closeMenuItem.setMnemonic('C');
271 outputTextboxMenu.setMnemonic('T');
272 undoMenuItem.setMnemonic('Z');
273 redoMenuItem.setMnemonic('0');
274 copy.setMnemonic('C');
275 cut.setMnemonic('U');
276 pasteMenu.setMnemonic('P');
277 reload.setMnemonic('R');
280 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
282 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
283 .getUserColourSchemes().keys();
285 while (userColours.hasMoreElements())
287 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
288 userColours.nextElement().toString());
289 radioItem.setName("USER_DEFINED");
290 radioItem.addMouseListener(new MouseAdapter()
293 public void mousePressed(MouseEvent evt)
295 if (evt.isPopupTrigger())
297 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
299 int option = JOptionPane.showInternalConfirmDialog(
300 jalview.gui.Desktop.desktop,
302 .getString("label.remove_from_default_list"),
304 .getString("label.remove_user_defined_colour"),
305 JOptionPane.YES_NO_OPTION);
306 if (option == JOptionPane.YES_OPTION)
308 jalview.gui.UserDefinedColours
309 .removeColourFromDefaults(radioItem.getText());
310 colourMenu.remove(radioItem);
314 radioItem.addActionListener(new ActionListener()
317 public void actionPerformed(ActionEvent evt)
319 userDefinedColour_actionPerformed(evt);
326 radioItem.addActionListener(new ActionListener()
329 public void actionPerformed(ActionEvent evt)
331 userDefinedColour_actionPerformed(evt);
334 colourMenu.insert(radioItem, 15);
335 colours.add(radioItem);
338 colours.add(noColourmenuItem);
339 colours.add(clustalColour);
340 colours.add(zappoColour);
341 colours.add(taylorColour);
342 colours.add(hydrophobicityColour);
343 colours.add(helixColour);
344 colours.add(strandColour);
345 colours.add(turnColour);
346 colours.add(buriedColour);
347 colours.add(userDefinedColour);
348 colours.add(PIDColour);
349 colours.add(BLOSUM62Colour);
350 colours.add(nucleotideColour);
351 colours.add(purinePyrimidineColour);
352 // colours.add(covariationColour);
353 colours.add(tcoffeeColour);
354 colours.add(RNAInteractionColour);
355 setColourSelected(jalview.bin.Cache.getDefault(
356 Preferences.DEFAULT_COLOUR, "None"));
359 public void setColourSelected(String defaultColour)
362 if (defaultColour != null)
364 int index = ColourSchemeProperty
365 .getColourIndexFromName(defaultColour);
369 case ColourSchemeProperty.CLUSTAL:
370 clustalColour.setSelected(true);
374 case ColourSchemeProperty.BLOSUM:
375 BLOSUM62Colour.setSelected(true);
379 case ColourSchemeProperty.PID:
380 PIDColour.setSelected(true);
384 case ColourSchemeProperty.ZAPPO:
385 zappoColour.setSelected(true);
389 case ColourSchemeProperty.TAYLOR:
390 taylorColour.setSelected(true);
393 case ColourSchemeProperty.HYDROPHOBIC:
394 hydrophobicityColour.setSelected(true);
398 case ColourSchemeProperty.HELIX:
399 helixColour.setSelected(true);
403 case ColourSchemeProperty.STRAND:
404 strandColour.setSelected(true);
408 case ColourSchemeProperty.TURN:
409 turnColour.setSelected(true);
413 case ColourSchemeProperty.BURIED:
414 buriedColour.setSelected(true);
418 case ColourSchemeProperty.NUCLEOTIDE:
419 nucleotideColour.setSelected(true);
423 case ColourSchemeProperty.TCOFFEE:
424 tcoffeeColour.setSelected(true);
427 case ColourSchemeProperty.PURINEPYRIMIDINE:
428 purinePyrimidineColour.setSelected(true);
432 case ColourSchemeProperty.RNAINTERACTION:
433 RNAInteractionColour.setSelected(true);
437 * case ColourSchemeProperty.COVARIATION:
438 * covariationColour.setSelected(true);
442 case ColourSchemeProperty.USER_DEFINED:
443 userDefinedColour.setSelected(true);
446 case ColourSchemeProperty.NONE:
448 noColourmenuItem.setSelected(true);
456 private void jbInit() throws Exception
458 JMenuItem saveAs = new JMenuItem(
459 MessageManager.getString("action.save_as"));
460 ActionListener al = new ActionListener()
463 public void actionPerformed(ActionEvent e)
465 saveAs_actionPerformed(e);
468 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
469 .getDefaultToolkit().getMenuShortcutKeyMask()
470 | KeyEvent.SHIFT_MASK, false);
471 addMenuActionAndAccelerator(keyStroke, saveAs, al);
473 closeMenuItem.setText(MessageManager.getString("action.close"));
474 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
475 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
476 al = new ActionListener()
479 public void actionPerformed(ActionEvent e)
481 closeMenuItem_actionPerformed(false);
484 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
486 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
487 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
488 JMenu annotationsMenu = new JMenu(
489 MessageManager.getString("action.annotations"));
490 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
491 colourMenu.setText(MessageManager.getString("action.colour"));
492 JMenu calculateMenu = new JMenu(
493 MessageManager.getString("action.calculate"));
494 webService.setText(MessageManager.getString("action.web_service"));
495 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
496 MessageManager.getString("action.select_all"));
497 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
498 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
499 al = new ActionListener()
502 public void actionPerformed(ActionEvent e)
504 selectAllSequenceMenuItem_actionPerformed(e);
507 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
509 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
510 MessageManager.getString("action.deselect_all"));
511 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
512 al = new ActionListener()
515 public void actionPerformed(ActionEvent e)
517 deselectAllSequenceMenuItem_actionPerformed(e);
520 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
522 JMenuItem invertSequenceMenuItem = new JMenuItem(
523 MessageManager.getString("action.invert_sequence_selection"));
524 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
525 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
526 al = new ActionListener()
529 public void actionPerformed(ActionEvent e)
531 invertSequenceMenuItem_actionPerformed(e);
534 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
536 JMenuItem grpsFromSelection = new JMenuItem(
537 MessageManager.getString("action.make_groups_selection"));
538 grpsFromSelection.addActionListener(new ActionListener()
541 public void actionPerformed(ActionEvent e)
543 makeGrpsFromSelection_actionPerformed(e);
546 JMenuItem expandAlignment = new JMenuItem(
547 MessageManager.getString("action.view_flanking_regions"));
548 expandAlignment.setToolTipText(MessageManager
549 .getString("label.view_flanking_regions"));
550 expandAlignment.addActionListener(new ActionListener()
553 public void actionPerformed(ActionEvent e)
558 JMenuItem remove2LeftMenuItem = new JMenuItem(
559 MessageManager.getString("action.remove_left"));
560 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
561 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
562 al = new ActionListener()
565 public void actionPerformed(ActionEvent e)
567 remove2LeftMenuItem_actionPerformed(e);
570 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
572 JMenuItem remove2RightMenuItem = new JMenuItem(
573 MessageManager.getString("action.remove_right"));
574 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
575 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
576 al = new ActionListener()
579 public void actionPerformed(ActionEvent e)
581 remove2RightMenuItem_actionPerformed(e);
584 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
586 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
587 MessageManager.getString("action.remove_empty_columns"));
588 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
589 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
590 al = new ActionListener()
593 public void actionPerformed(ActionEvent e)
595 removeGappedColumnMenuItem_actionPerformed(e);
598 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
600 JMenuItem removeAllGapsMenuItem = new JMenuItem(
601 MessageManager.getString("action.remove_all_gaps"));
602 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
603 .getDefaultToolkit().getMenuShortcutKeyMask()
604 | KeyEvent.SHIFT_MASK, false);
605 al = new ActionListener()
608 public void actionPerformed(ActionEvent e)
610 removeAllGapsMenuItem_actionPerformed(e);
613 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
615 JMenuItem justifyLeftMenuItem = new JMenuItem(
616 MessageManager.getString("action.left_justify_alignment"));
617 justifyLeftMenuItem.addActionListener(new ActionListener()
620 public void actionPerformed(ActionEvent e)
622 justifyLeftMenuItem_actionPerformed(e);
625 JMenuItem justifyRightMenuItem = new JMenuItem(
626 MessageManager.getString("action.right_justify_alignment"));
627 justifyRightMenuItem.addActionListener(new ActionListener()
630 public void actionPerformed(ActionEvent e)
632 justifyRightMenuItem_actionPerformed(e);
635 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
636 viewBoxesMenuItem.setState(true);
637 viewBoxesMenuItem.addActionListener(new ActionListener()
640 public void actionPerformed(ActionEvent e)
642 viewBoxesMenuItem_actionPerformed(e);
645 viewTextMenuItem.setText(MessageManager.getString("action.text"));
646 viewTextMenuItem.setState(true);
647 viewTextMenuItem.addActionListener(new ActionListener()
650 public void actionPerformed(ActionEvent e)
652 viewTextMenuItem_actionPerformed(e);
655 showNonconservedMenuItem.setText(MessageManager
656 .getString("label.show_non_conversed"));
657 showNonconservedMenuItem.setState(false);
658 showNonconservedMenuItem.addActionListener(new ActionListener()
661 public void actionPerformed(ActionEvent e)
663 showUnconservedMenuItem_actionPerformed(e);
666 JMenuItem sortPairwiseMenuItem = new JMenuItem(
667 MessageManager.getString("action.by_pairwise_id"));
668 sortPairwiseMenuItem.addActionListener(new ActionListener()
671 public void actionPerformed(ActionEvent e)
673 sortPairwiseMenuItem_actionPerformed(e);
676 JMenuItem sortIDMenuItem = new JMenuItem(
677 MessageManager.getString("action.by_id"));
678 sortIDMenuItem.addActionListener(new ActionListener()
681 public void actionPerformed(ActionEvent e)
683 sortIDMenuItem_actionPerformed(e);
686 JMenuItem sortLengthMenuItem = new JMenuItem(
687 MessageManager.getString("action.by_length"));
688 sortLengthMenuItem.addActionListener(new ActionListener()
691 public void actionPerformed(ActionEvent e)
693 sortLengthMenuItem_actionPerformed(e);
696 JMenuItem sortGroupMenuItem = new JMenuItem(
697 MessageManager.getString("action.by_group"));
698 sortGroupMenuItem.addActionListener(new ActionListener()
701 public void actionPerformed(ActionEvent e)
703 sortGroupMenuItem_actionPerformed(e);
707 JMenuItem removeRedundancyMenuItem = new JMenuItem(
708 MessageManager.getString("action.remove_redundancy"));
709 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
710 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
711 al = new ActionListener()
714 public void actionPerformed(ActionEvent e)
716 removeRedundancyMenuItem_actionPerformed(e);
719 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
721 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
722 MessageManager.getString("action.pairwise_alignment"));
723 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
726 public void actionPerformed(ActionEvent e)
728 pairwiseAlignmentMenuItem_actionPerformed(e);
731 JMenuItem PCAMenuItem = new JMenuItem(
732 MessageManager.getString("label.principal_component_analysis"));
733 PCAMenuItem.addActionListener(new ActionListener()
736 public void actionPerformed(ActionEvent e)
738 PCAMenuItem_actionPerformed(e);
741 JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
742 MessageManager.getString("label.average_distance_identity"));
743 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
746 public void actionPerformed(ActionEvent e)
748 averageDistanceTreeMenuItem_actionPerformed(e);
751 JMenuItem neighbourTreeMenuItem = new JMenuItem(
752 MessageManager.getString("label.neighbour_joining_identity"));
753 neighbourTreeMenuItem.addActionListener(new ActionListener()
756 public void actionPerformed(ActionEvent e)
758 neighbourTreeMenuItem_actionPerformed(e);
762 this.getContentPane().setLayout(new BorderLayout());
763 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
764 statusBar.setBackground(Color.white);
765 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
766 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
767 statusBar.setText(MessageManager.getString("label.status_bar"));
768 outputTextboxMenu.setText(MessageManager
769 .getString("label.out_to_textbox"));
770 clustalColour.setText(MessageManager.getString("label.clustalx"));
771 clustalColour.addActionListener(new ActionListener()
774 public void actionPerformed(ActionEvent e)
776 clustalColour_actionPerformed(e);
779 zappoColour.setText(MessageManager.getString("label.zappo"));
780 zappoColour.addActionListener(new ActionListener()
783 public void actionPerformed(ActionEvent e)
785 zappoColour_actionPerformed(e);
788 taylorColour.setText(MessageManager.getString("label.taylor"));
789 taylorColour.addActionListener(new ActionListener()
792 public void actionPerformed(ActionEvent e)
794 taylorColour_actionPerformed(e);
797 hydrophobicityColour.setText(MessageManager
798 .getString("label.hydrophobicity"));
799 hydrophobicityColour.addActionListener(new ActionListener()
802 public void actionPerformed(ActionEvent e)
804 hydrophobicityColour_actionPerformed(e);
807 helixColour.setText(MessageManager.getString("label.helix_propensity"));
808 helixColour.addActionListener(new ActionListener()
811 public void actionPerformed(ActionEvent e)
813 helixColour_actionPerformed(e);
816 strandColour.setText(MessageManager
817 .getString("label.strand_propensity"));
818 strandColour.addActionListener(new ActionListener()
821 public void actionPerformed(ActionEvent e)
823 strandColour_actionPerformed(e);
826 turnColour.setText(MessageManager.getString("label.turn_propensity"));
827 turnColour.addActionListener(new ActionListener()
830 public void actionPerformed(ActionEvent e)
832 turnColour_actionPerformed(e);
835 buriedColour.setText(MessageManager.getString("label.buried_index"));
836 buriedColour.addActionListener(new ActionListener()
839 public void actionPerformed(ActionEvent e)
841 buriedColour_actionPerformed(e);
844 userDefinedColour.setText(MessageManager
845 .getString("action.user_defined"));
846 userDefinedColour.addActionListener(new ActionListener()
849 public void actionPerformed(ActionEvent e)
851 userDefinedColour_actionPerformed(e);
855 .setText(MessageManager.getString("label.percentage_identity"));
856 PIDColour.addActionListener(new ActionListener()
859 public void actionPerformed(ActionEvent e)
861 PIDColour_actionPerformed(e);
865 .setText(MessageManager.getString("label.blosum62_score"));
866 BLOSUM62Colour.addActionListener(new ActionListener()
869 public void actionPerformed(ActionEvent e)
871 BLOSUM62Colour_actionPerformed(e);
874 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
875 nucleotideColour.addActionListener(new ActionListener()
878 public void actionPerformed(ActionEvent e)
880 nucleotideColour_actionPerformed(e);
884 purinePyrimidineColour.setText(MessageManager
885 .getString("label.purine_pyrimidine"));
886 purinePyrimidineColour.addActionListener(new ActionListener()
889 public void actionPerformed(ActionEvent e)
891 purinePyrimidineColour_actionPerformed(e);
895 RNAInteractionColour.setText("RNA Interaction type");
896 RNAInteractionColour.addActionListener(new ActionListener()
899 public void actionPerformed(ActionEvent e)
901 RNAInteractionColour_actionPerformed(e);
905 * covariationColour.setText("Covariation");
906 * covariationColour.addActionListener(new ActionListener() { public void
907 * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
911 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
912 MessageManager.getString("label.average_distance_bloslum62"));
913 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
916 public void actionPerformed(ActionEvent e)
918 avTreeBlosumMenuItem_actionPerformed(e);
921 JMenuItem njTreeBlosumMenuItem = new JMenuItem(
922 MessageManager.getString("label.neighbour_blosum62"));
923 njTreeBlosumMenuItem.addActionListener(new ActionListener()
926 public void actionPerformed(ActionEvent e)
928 njTreeBlosumMenuItem_actionPerformed(e);
931 annotationPanelMenuItem.setActionCommand("");
932 annotationPanelMenuItem.setText(MessageManager
933 .getString("label.show_annotations"));
934 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
936 annotationPanelMenuItem.addActionListener(new ActionListener()
939 public void actionPerformed(ActionEvent e)
941 annotationPanelMenuItem_actionPerformed(e);
944 showAllAlAnnotations.setText(MessageManager
945 .getString("label.show_all_al_annotations"));
946 final boolean isAnnotationPanelShown = annotationPanelMenuItem
948 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
949 showAllAlAnnotations.addActionListener(new ActionListener()
952 public void actionPerformed(ActionEvent e)
954 showAllAnnotations_actionPerformed(false, true);
957 hideAllAlAnnotations.setText(MessageManager
958 .getString("label.hide_all_al_annotations"));
959 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
960 hideAllAlAnnotations.addActionListener(new ActionListener()
963 public void actionPerformed(ActionEvent e)
965 hideAllAnnotations_actionPerformed(false, true);
968 showAllSeqAnnotations.setText(MessageManager
969 .getString("label.show_all_seq_annotations"));
970 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
971 showAllSeqAnnotations.addActionListener(new ActionListener()
974 public void actionPerformed(ActionEvent e)
976 showAllAnnotations_actionPerformed(true, false);
979 hideAllSeqAnnotations.setText(MessageManager
980 .getString("label.hide_all_seq_annotations"));
981 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
982 hideAllSeqAnnotations.addActionListener(new ActionListener()
985 public void actionPerformed(ActionEvent e)
987 hideAllAnnotations_actionPerformed(true, false);
990 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
991 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
992 SequenceAnnotationOrder.NONE.name()));
993 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
994 MessageManager.getString("label.sort_annotations_by_sequence"));
995 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
996 MessageManager.getString("label.sort_annotations_by_label"));
999 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1000 sortAnnBySequence.addActionListener(new ActionListener()
1003 public void actionPerformed(ActionEvent e)
1005 boolean newState = sortAnnBySequence.getState();
1006 sortAnnByLabel.setSelected(false);
1007 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1008 : SequenceAnnotationOrder.NONE);
1009 sortAnnotations_actionPerformed();
1013 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1014 sortAnnByLabel.addActionListener(new ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 boolean newState = sortAnnByLabel.getState();
1020 sortAnnBySequence.setSelected(false);
1021 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1022 : SequenceAnnotationOrder.NONE);
1023 sortAnnotations_actionPerformed();
1026 colourTextMenuItem.setText(MessageManager
1027 .getString("label.colour_text"));
1028 colourTextMenuItem.addActionListener(new ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 colourTextMenuItem_actionPerformed(e);
1037 JMenuItem htmlMenuItem = new JMenuItem(
1038 MessageManager.getString("label.html"));
1039 htmlMenuItem.addActionListener(new ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 htmlMenuItem_actionPerformed(e);
1048 JMenuItem createBioJS = new JMenuItem(
1049 MessageManager.getString("label.biojs_html_export"));
1050 createBioJS.addActionListener(new java.awt.event.ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 bioJSMenuItem_actionPerformed(e);
1059 JMenuItem overviewMenuItem = new JMenuItem(
1060 MessageManager.getString("label.overview_window"));
1061 overviewMenuItem.addActionListener(new ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 overviewMenuItem_actionPerformed(e);
1070 undoMenuItem.setEnabled(false);
1071 undoMenuItem.setText(MessageManager.getString("action.undo"));
1072 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
1073 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1074 al = new ActionListener()
1077 public void actionPerformed(ActionEvent e)
1079 undoMenuItem_actionPerformed(e);
1082 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
1084 redoMenuItem.setEnabled(false);
1085 redoMenuItem.setText(MessageManager.getString("action.redo"));
1086 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
1087 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1088 al = new ActionListener()
1091 public void actionPerformed(ActionEvent e)
1093 redoMenuItem_actionPerformed(e);
1096 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
1098 conservationMenuItem.setText(MessageManager
1099 .getString("action.by_conservation"));
1100 conservationMenuItem.addActionListener(new ActionListener()
1103 public void actionPerformed(ActionEvent e)
1105 conservationMenuItem_actionPerformed(e);
1108 noColourmenuItem.setText(MessageManager.getString("label.none"));
1109 noColourmenuItem.addActionListener(new ActionListener()
1112 public void actionPerformed(ActionEvent e)
1114 noColourmenuItem_actionPerformed(e);
1117 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1118 wrapMenuItem.addActionListener(new ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 wrapMenuItem_actionPerformed(e);
1127 JMenuItem printMenuItem = new JMenuItem(
1128 MessageManager.getString("action.print"));
1129 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
1130 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1131 al = new ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 printMenuItem_actionPerformed(e);
1139 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
1142 .setText(MessageManager.getString("action.show_gaps"));
1143 renderGapsMenuItem.setState(true);
1144 renderGapsMenuItem.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent e)
1149 renderGapsMenuItem_actionPerformed(e);
1153 JMenuItem findMenuItem = new JMenuItem(
1154 MessageManager.getString("action.find"));
1155 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
1156 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1157 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1158 MessageManager.getString("label.find_tip")));
1159 al = new ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 findMenuItem_actionPerformed(e);
1167 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
1169 abovePIDThreshold.setText(MessageManager
1170 .getString("label.above_identity_threshold"));
1171 abovePIDThreshold.addActionListener(new ActionListener()
1174 public void actionPerformed(ActionEvent e)
1176 abovePIDThreshold_actionPerformed(e);
1179 showSeqFeatures.setText(MessageManager
1180 .getString("label.show_sequence_features"));
1181 showSeqFeatures.addActionListener(new ActionListener()
1184 public void actionPerformed(ActionEvent actionEvent)
1186 showSeqFeatures_actionPerformed(actionEvent);
1190 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1191 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1192 * void actionPerformed(ActionEvent actionEvent) {
1193 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1195 showDbRefsMenuitem.setText(MessageManager
1196 .getString("label.show_database_refs"));
1197 showDbRefsMenuitem.addActionListener(new ActionListener()
1201 public void actionPerformed(ActionEvent e)
1203 showDbRefs_actionPerformed(e);
1207 showNpFeatsMenuitem.setText(MessageManager
1208 .getString("label.show_non_positional_features"));
1209 showNpFeatsMenuitem.addActionListener(new ActionListener()
1213 public void actionPerformed(ActionEvent e)
1215 showNpFeats_actionPerformed(e);
1219 showGroupConservation.setText(MessageManager
1220 .getString("label.group_conservation"));
1221 showGroupConservation.addActionListener(new ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 showGroupConservation_actionPerformed(e);
1232 showGroupConsensus.setText(MessageManager
1233 .getString("label.group_consensus"));
1234 showGroupConsensus.addActionListener(new ActionListener()
1238 public void actionPerformed(ActionEvent e)
1240 showGroupConsensus_actionPerformed(e);
1244 showConsensusHistogram.setText(MessageManager
1245 .getString("label.show_consensus_histogram"));
1246 showConsensusHistogram.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 showConsensusHistogram_actionPerformed(e);
1256 showSequenceLogo.setText(MessageManager
1257 .getString("label.show_consensus_logo"));
1258 showSequenceLogo.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 showSequenceLogo_actionPerformed(e);
1268 normaliseSequenceLogo.setText(MessageManager
1269 .getString("label.norm_consensus_logo"));
1270 normaliseSequenceLogo.addActionListener(new ActionListener()
1274 public void actionPerformed(ActionEvent e)
1276 normaliseSequenceLogo_actionPerformed(e);
1280 applyAutoAnnotationSettings.setText(MessageManager
1281 .getString("label.apply_all_groups"));
1282 applyAutoAnnotationSettings.setState(false);
1283 applyAutoAnnotationSettings.setVisible(true);
1284 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1287 public void actionPerformed(ActionEvent e)
1289 applyAutoAnnotationSettings_actionPerformed(e);
1293 ButtonGroup buttonGroup = new ButtonGroup();
1294 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
1295 MessageManager.getString("label.show_first"));
1296 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
1297 MessageManager.getString("label.show_last"));
1298 buttonGroup.add(showAutoFirst);
1299 buttonGroup.add(showAutoLast);
1300 final boolean autoFirst = Cache.getDefault(
1301 Preferences.SHOW_AUTOCALC_ABOVE, false);
1302 showAutoFirst.setSelected(autoFirst);
1303 setShowAutoCalculatedAbove(autoFirst);
1304 showAutoFirst.addActionListener(new ActionListener()
1307 public void actionPerformed(ActionEvent e)
1309 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1310 sortAnnotations_actionPerformed();
1313 showAutoLast.setSelected(!showAutoFirst.isSelected());
1314 showAutoLast.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent e)
1319 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1320 sortAnnotations_actionPerformed();
1324 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1325 nucleotideColour.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 nucleotideColour_actionPerformed(e);
1334 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1335 tcoffeeColour.setEnabled(false);
1336 tcoffeeColour.addActionListener(new ActionListener()
1340 public void actionPerformed(ActionEvent e)
1342 tcoffeeColorScheme_actionPerformed(e);
1346 JMenuItem deleteGroups = new JMenuItem(
1347 MessageManager.getString("action.undefine_groups"));
1348 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1349 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1350 al = new ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 deleteGroups_actionPerformed(e);
1358 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1360 JMenuItem createGroup = new JMenuItem(
1361 MessageManager.getString("action.create_groups"));
1362 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1363 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1364 al = new ActionListener()
1367 public void actionPerformed(ActionEvent e)
1369 createGroup_actionPerformed(e);
1372 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1374 JMenuItem unGroup = new JMenuItem(
1375 MessageManager.getString("action.remove_group"));
1376 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1377 .getDefaultToolkit().getMenuShortcutKeyMask()
1378 | KeyEvent.SHIFT_MASK, false);
1379 al = new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 unGroup_actionPerformed(e);
1387 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1389 copy.setText(MessageManager.getString("action.copy"));
1390 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1391 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1393 al = new ActionListener()
1396 public void actionPerformed(ActionEvent e)
1398 copy_actionPerformed(e);
1401 addMenuActionAndAccelerator(keyStroke, copy, al);
1403 cut.setText(MessageManager.getString("action.cut"));
1404 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1405 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1406 al = new ActionListener()
1409 public void actionPerformed(ActionEvent e)
1411 cut_actionPerformed(e);
1414 addMenuActionAndAccelerator(keyStroke, cut, al);
1416 JMenuItem delete = new JMenuItem(
1417 MessageManager.getString("action.delete"));
1418 delete.addActionListener(new ActionListener()
1421 public void actionPerformed(ActionEvent e)
1423 delete_actionPerformed(e);
1427 pasteMenu.setText(MessageManager.getString("action.paste"));
1428 JMenuItem pasteNew = new JMenuItem(
1429 MessageManager.getString("label.to_new_alignment"));
1430 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1431 .getDefaultToolkit().getMenuShortcutKeyMask()
1432 | KeyEvent.SHIFT_MASK, false);
1433 al = new ActionListener()
1436 public void actionPerformed(ActionEvent e)
1438 pasteNew_actionPerformed(e);
1441 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1443 JMenuItem pasteThis = new JMenuItem(
1444 MessageManager.getString("label.to_this_alignment"));
1445 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1446 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1447 al = new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 pasteThis_actionPerformed(e);
1455 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1457 applyToAllGroups.setText(MessageManager
1458 .getString("label.apply_colour_to_all_groups"));
1459 applyToAllGroups.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 applyToAllGroups_actionPerformed(e);
1467 JMenuItem createPNG = new JMenuItem("PNG");
1468 createPNG.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent e)
1476 createPNG.setActionCommand(MessageManager
1477 .getString("label.save_png_image"));
1479 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1480 font.addActionListener(new ActionListener()
1483 public void actionPerformed(ActionEvent e)
1485 font_actionPerformed(e);
1488 seqLimits.setText(MessageManager
1489 .getString("label.show_sequence_limits"));
1490 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1491 seqLimits.addActionListener(new ActionListener()
1494 public void actionPerformed(ActionEvent e)
1496 seqLimit_actionPerformed(e);
1499 JMenuItem epsFile = new JMenuItem("EPS");
1500 epsFile.addActionListener(new ActionListener()
1503 public void actionPerformed(ActionEvent e)
1509 JMenuItem createSVG = new JMenuItem("SVG");
1510 createSVG.addActionListener(new ActionListener()
1513 public void actionPerformed(ActionEvent e)
1519 JMenuItem loadTreeMenuItem = new JMenuItem(
1520 MessageManager.getString("label.load_associated_tree"));
1521 loadTreeMenuItem.setActionCommand(MessageManager
1522 .getString("label.load_tree_for_sequence_set"));
1523 loadTreeMenuItem.addActionListener(new ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 loadTreeMenuItem_actionPerformed(e);
1532 scaleAbove.setVisible(false);
1533 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1534 scaleAbove.addActionListener(new ActionListener()
1537 public void actionPerformed(ActionEvent e)
1539 scaleAbove_actionPerformed(e);
1542 scaleLeft.setVisible(false);
1543 scaleLeft.setSelected(true);
1544 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1545 scaleLeft.addActionListener(new ActionListener()
1548 public void actionPerformed(ActionEvent e)
1550 scaleLeft_actionPerformed(e);
1553 scaleRight.setVisible(false);
1554 scaleRight.setSelected(true);
1555 scaleRight.setText(MessageManager.getString("action.scale_right"));
1556 scaleRight.addActionListener(new ActionListener()
1559 public void actionPerformed(ActionEvent e)
1561 scaleRight_actionPerformed(e);
1564 centreColumnLabelsMenuItem.setVisible(true);
1565 centreColumnLabelsMenuItem.setState(false);
1566 centreColumnLabelsMenuItem.setText(MessageManager
1567 .getString("label.centre_column_labels"));
1568 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 centreColumnLabels_actionPerformed(e);
1576 followHighlightMenuItem.setVisible(true);
1577 followHighlightMenuItem.setState(true);
1578 followHighlightMenuItem.setText(MessageManager
1579 .getString("label.automatic_scrolling"));
1580 followHighlightMenuItem.addActionListener(new ActionListener()
1584 public void actionPerformed(ActionEvent e)
1586 followHighlight_actionPerformed();
1591 JMenuItem modifyPID = new JMenuItem(
1592 MessageManager.getString("label.modify_identity_threshold"));
1593 modifyPID.addActionListener(new ActionListener()
1596 public void actionPerformed(ActionEvent e)
1598 modifyPID_actionPerformed(e);
1601 modifyConservation.setText(MessageManager
1602 .getString("label.modify_conservation_threshold"));
1603 modifyConservation.addActionListener(new ActionListener()
1606 public void actionPerformed(ActionEvent e)
1608 modifyConservation_actionPerformed(e);
1612 .setText(MessageManager.getString("action.by_tree_order"));
1613 sort.setText(MessageManager.getString("action.sort"));
1614 sort.addMenuListener(new MenuListener()
1617 public void menuSelected(MenuEvent e)
1623 public void menuDeselected(MenuEvent e)
1628 public void menuCanceled(MenuEvent e)
1632 sortByAnnotScore.setText(MessageManager
1633 .getString("label.sort_by_score"));
1634 sort.add(sortByAnnotScore);
1635 sort.addMenuListener(new javax.swing.event.MenuListener()
1639 public void menuCanceled(MenuEvent e)
1644 public void menuDeselected(MenuEvent e)
1649 public void menuSelected(MenuEvent e)
1651 buildSortByAnnotationScoresMenu();
1654 sortByAnnotScore.setVisible(false);
1657 .setText(MessageManager.getString("action.calculate_tree"));
1659 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1660 padGapsMenuitem.setState(jalview.bin.Cache
1661 .getDefault("PAD_GAPS", false));
1662 padGapsMenuitem.addActionListener(new ActionListener()
1665 public void actionPerformed(ActionEvent e)
1667 padGapsMenuitem_actionPerformed(e);
1670 JMenuItem vamsasStore = new JMenuItem(
1671 MessageManager.getString("label.vamsas_store"));
1672 vamsasStore.setVisible(false);
1673 vamsasStore.addActionListener(new ActionListener()
1676 public void actionPerformed(ActionEvent e)
1678 vamsasStore_actionPerformed(e);
1681 showTranslation.setText(MessageManager
1682 .getString("label.translate_cDNA"));
1683 showTranslation.addActionListener(new ActionListener()
1686 public void actionPerformed(ActionEvent e)
1688 showTranslation_actionPerformed(e);
1691 showReverse.setText(MessageManager.getString("label.reverse"));
1692 showReverse.addActionListener(new ActionListener()
1695 public void actionPerformed(ActionEvent e)
1697 showReverse_actionPerformed(false);
1700 showReverseComplement.setText(MessageManager
1701 .getString("label.reverse_complement"));
1702 showReverseComplement.addActionListener(new ActionListener()
1705 public void actionPerformed(ActionEvent e)
1707 showReverse_actionPerformed(true);
1711 JMenuItem extractScores = new JMenuItem(
1712 MessageManager.getString("label.extract_scores"));
1713 extractScores.addActionListener(new ActionListener()
1716 public void actionPerformed(ActionEvent e)
1718 extractScores_actionPerformed(e);
1721 extractScores.setVisible(true);
1722 // JBPNote: TODO: make gui for regex based score extraction
1724 // for show products actions see AlignFrame.canShowProducts
1725 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1727 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1728 runGroovy.setToolTipText(MessageManager.getString("label.run_groovy_tip"));
1729 runGroovy.addActionListener(new ActionListener()
1732 public void actionPerformed(ActionEvent e)
1734 runGroovy_actionPerformed();
1738 JMenuItem openFeatureSettings = new JMenuItem(
1739 MessageManager.getString("action.feature_settings"));
1740 openFeatureSettings.addActionListener(new ActionListener()
1743 public void actionPerformed(ActionEvent e)
1745 featureSettings_actionPerformed(e);
1748 JMenuItem fetchSequence = new JMenuItem(
1749 MessageManager.getString("label.fetch_sequences"));
1750 fetchSequence.addActionListener(new ActionListener()
1753 public void actionPerformed(ActionEvent e)
1755 fetchSequence_actionPerformed(e);
1759 JMenuItem annotationColour = new JMenuItem(
1760 MessageManager.getString("action.by_annotation"));
1761 annotationColour.addActionListener(new ActionListener()
1764 public void actionPerformed(ActionEvent e)
1766 annotationColour_actionPerformed(e);
1770 JMenuItem annotationColumn = new JMenuItem(
1771 MessageManager.getString("action.select_by_annotation"));
1772 annotationColumn.addActionListener(new ActionListener()
1775 public void actionPerformed(ActionEvent e)
1777 annotationColumn_actionPerformed(e);
1781 rnahelicesColour.setText(MessageManager
1782 .getString("action.by_rna_helixes"));
1783 rnahelicesColour.addActionListener(new ActionListener()
1786 public void actionPerformed(ActionEvent e)
1788 rnahelicesColour_actionPerformed(e);
1792 JMenuItem associatedData = new JMenuItem(
1793 MessageManager.getString("label.load_features_annotations"));
1794 associatedData.addActionListener(new ActionListener()
1797 public void actionPerformed(ActionEvent e)
1799 associatedData_actionPerformed(e);
1802 autoCalculate.setText(MessageManager
1803 .getString("label.autocalculate_consensus"));
1804 autoCalculate.setState(jalview.bin.Cache.getDefault(
1805 "AUTO_CALC_CONSENSUS", true));
1806 autoCalculate.addActionListener(new ActionListener()
1809 public void actionPerformed(ActionEvent e)
1811 autoCalculate_actionPerformed(e);
1814 sortByTree.setText(MessageManager
1815 .getString("label.sort_alignment_new_tree"));
1817 .setToolTipText("<html>"
1819 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1821 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1822 sortByTree.addActionListener(new ActionListener()
1825 public void actionPerformed(ActionEvent e)
1827 sortByTreeOption_actionPerformed(e);
1831 listenToViewSelections.setText(MessageManager
1832 .getString("label.listen_for_selections"));
1833 listenToViewSelections
1834 .setToolTipText("<html>"
1836 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1837 listenToViewSelections.setState(false);
1838 listenToViewSelections.addActionListener(new ActionListener()
1841 public void actionPerformed(ActionEvent e)
1843 listenToViewSelections_actionPerformed(e);
1847 JMenu addSequenceMenu = new JMenu(
1848 MessageManager.getString("label.add_sequences"));
1849 JMenuItem addFromFile = new JMenuItem(
1850 MessageManager.getString("label.from_file"));
1851 addFromFile.addActionListener(new ActionListener()
1854 public void actionPerformed(ActionEvent e)
1856 addFromFile_actionPerformed(e);
1859 JMenuItem addFromText = new JMenuItem(
1860 MessageManager.getString("label.from_textbox"));
1861 addFromText.addActionListener(new ActionListener()
1864 public void actionPerformed(ActionEvent e)
1866 addFromText_actionPerformed(e);
1869 JMenuItem addFromURL = new JMenuItem(
1870 MessageManager.getString("label.from_url"));
1871 addFromURL.addActionListener(new ActionListener()
1874 public void actionPerformed(ActionEvent e)
1876 addFromURL_actionPerformed(e);
1879 JMenuItem exportFeatures = new JMenuItem(
1880 MessageManager.getString("label.export_features"));
1881 exportFeatures.addActionListener(new ActionListener()
1884 public void actionPerformed(ActionEvent e)
1886 exportFeatures_actionPerformed(e);
1889 JMenuItem exportAnnotations = new JMenuItem(
1890 MessageManager.getString("label.export_annotations"));
1891 exportAnnotations.addActionListener(new ActionListener()
1894 public void actionPerformed(ActionEvent e)
1896 exportAnnotations_actionPerformed(e);
1899 statusPanel.setLayout(new GridLayout());
1900 JMenuItem showAllSeqs = new JMenuItem(
1901 MessageManager.getString("label.all_sequences"));
1902 showAllSeqs.setToolTipText(MessageManager
1903 .getString("label.toggle_sequence_visibility"));
1904 showAllSeqs.addActionListener(new ActionListener()
1907 public void actionPerformed(ActionEvent e)
1909 showAllSeqs_actionPerformed(e);
1912 JMenuItem showAllColumns = new JMenuItem(
1913 MessageManager.getString("label.all_columns"));
1914 showAllColumns.setToolTipText(MessageManager
1915 .getString("label.toggle_columns_visibility"));
1916 showAllColumns.addActionListener(new ActionListener()
1919 public void actionPerformed(ActionEvent e)
1921 showAllColumns_actionPerformed(e);
1924 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1925 JMenuItem hideSelSequences = new JMenuItem(
1926 MessageManager.getString("label.selected_sequences"));
1927 hideSelSequences.setToolTipText(MessageManager
1928 .getString("label.toggle_sequence_visibility"));
1929 hideSelSequences.addActionListener(new ActionListener()
1932 public void actionPerformed(ActionEvent e)
1934 hideSelSequences_actionPerformed(e);
1937 JMenuItem hideSelColumns = new JMenuItem(
1938 MessageManager.getString("label.selected_columns"));
1939 hideSelColumns.setToolTipText(MessageManager
1940 .getString("label.toggle_columns_visibility"));
1941 hideSelColumns.addActionListener(new ActionListener()
1944 public void actionPerformed(ActionEvent e)
1946 hideSelColumns_actionPerformed(e);
1949 JMenuItem hideAllSelection = new JMenuItem(
1950 MessageManager.getString("label.selected_region"));
1951 hideAllSelection.addActionListener(new ActionListener()
1954 public void actionPerformed(ActionEvent e)
1956 hideAllSelection_actionPerformed(e);
1959 // TODO: should be hidden if no selection exists.
1960 JMenuItem hideAllButSelection = new JMenuItem(
1961 MessageManager.getString("label.all_but_selected_region"));
1962 hideAllButSelection.addActionListener(new ActionListener()
1965 public void actionPerformed(ActionEvent e)
1967 hideAllButSelection_actionPerformed(e);
1970 JMenuItem showAllhidden = new JMenuItem(
1971 MessageManager.getString("label.all_sequences_columns"));
1972 showAllhidden.setToolTipText(MessageManager
1973 .getString("label.toggles_visibility_hidden_selected_regions"));
1974 showAllhidden.addActionListener(new ActionListener()
1977 public void actionPerformed(ActionEvent e)
1979 showAllhidden_actionPerformed(e);
1982 hiddenMarkers.setText(MessageManager
1983 .getString("action.show_hidden_markers"));
1984 hiddenMarkers.addActionListener(new ActionListener()
1987 public void actionPerformed(ActionEvent e)
1989 hiddenMarkers_actionPerformed(e);
1993 JMenuItem invertColSel = new JMenuItem(
1994 MessageManager.getString("action.invert_column_selection"));
1995 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1996 .getDefaultToolkit().getMenuShortcutKeyMask()
1997 | KeyEvent.ALT_MASK, false);
1998 al = new ActionListener()
2001 public void actionPerformed(ActionEvent e)
2003 invertColSel_actionPerformed(e);
2006 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
2008 showComplementMenuItem.setVisible(false);
2009 showComplementMenuItem.addActionListener(new ActionListener()
2012 public void actionPerformed(ActionEvent e)
2014 showComplement_actionPerformed(showComplementMenuItem.getState());
2018 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2021 public void stateChanged(ChangeEvent evt)
2023 JTabbedPane pane = (JTabbedPane) evt.getSource();
2024 int sel = pane.getSelectedIndex();
2025 tabSelectionChanged(sel);
2028 tabbedPane.addMouseListener(new MouseAdapter()
2031 public void mousePressed(MouseEvent e)
2033 tabbedPane_mousePressed(e);
2036 tabbedPane.addFocusListener(new FocusAdapter()
2039 public void focusGained(FocusEvent e)
2041 tabbedPane_focusGained(e);
2045 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
2046 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
2047 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2048 al = new ActionListener()
2051 public void actionPerformed(ActionEvent e)
2053 save_actionPerformed(e);
2056 addMenuActionAndAccelerator(keyStroke, save, al);
2058 reload.setEnabled(false);
2059 reload.setText(MessageManager.getString("action.reload"));
2060 reload.addActionListener(new ActionListener()
2063 public void actionPerformed(ActionEvent e)
2065 reload_actionPerformed(e);
2069 JMenuItem newView = new JMenuItem(
2070 MessageManager.getString("action.new_view"));
2071 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
2072 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2073 al = new ActionListener()
2076 public void actionPerformed(ActionEvent e)
2078 newView_actionPerformed(e);
2081 addMenuActionAndAccelerator(keyStroke, newView, al);
2083 tabbedPane.setToolTipText("<html><i>"
2084 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2086 JMenuItem textColour = new JMenuItem(
2087 MessageManager.getString("action.set_text_colour"));
2088 textColour.addActionListener(new ActionListener()
2091 public void actionPerformed(ActionEvent e)
2093 textColour_actionPerformed(e);
2096 formatMenu.setText(MessageManager.getString("action.format"));
2097 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
2098 idRightAlign.setText(MessageManager
2099 .getString("label.right_align_sequence_id"));
2100 idRightAlign.addActionListener(new ActionListener()
2103 public void actionPerformed(ActionEvent e)
2105 idRightAlign_actionPerformed(e);
2109 gatherViews.setEnabled(false);
2110 gatherViews.setText(MessageManager.getString("action.gather_views"));
2111 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
2112 al = new ActionListener()
2115 public void actionPerformed(ActionEvent e)
2117 gatherViews_actionPerformed(e);
2120 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
2122 expandViews.setEnabled(false);
2123 expandViews.setText(MessageManager.getString("action.expand_views"));
2124 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
2125 al = new ActionListener()
2128 public void actionPerformed(ActionEvent e)
2130 expandViews_actionPerformed(e);
2133 addMenuActionAndAccelerator(keyStroke, expandViews, al);
2135 JMenuItem pageSetup = new JMenuItem(
2136 MessageManager.getString("action.page_setup"));
2137 pageSetup.addActionListener(new ActionListener()
2140 public void actionPerformed(ActionEvent e)
2142 pageSetup_actionPerformed(e);
2145 JMenuItem alignmentProperties = new JMenuItem(
2146 MessageManager.getString("label.alignment_props"));
2147 alignmentProperties.addActionListener(new ActionListener()
2150 public void actionPerformed(ActionEvent actionEvent)
2152 alignmentProperties();
2155 JMenu tooltipSettingsMenu = new JMenu(
2156 MessageManager.getString("label.sequence_id_tooltip"));
2157 JMenu autoAnnMenu = new JMenu(
2158 MessageManager.getString("label.autocalculated_annotation"));
2160 JMenu exportImageMenu = new JMenu(
2161 MessageManager.getString("label.export_image"));
2162 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
2163 alignFrameMenuBar.add(fileMenu);
2164 alignFrameMenuBar.add(editMenu);
2165 alignFrameMenuBar.add(selectMenu);
2166 alignFrameMenuBar.add(viewMenu);
2167 alignFrameMenuBar.add(annotationsMenu);
2168 alignFrameMenuBar.add(formatMenu);
2169 alignFrameMenuBar.add(colourMenu);
2170 alignFrameMenuBar.add(calculateMenu);
2171 alignFrameMenuBar.add(webService);
2173 fileMenu.add(fetchSequence);
2174 fileMenu.add(addSequenceMenu);
2175 fileMenu.add(reload);
2176 fileMenu.addSeparator();
2177 fileMenu.add(vamsasStore);
2179 fileMenu.add(saveAs);
2180 fileMenu.add(outputTextboxMenu);
2181 fileMenu.add(pageSetup);
2182 fileMenu.add(printMenuItem);
2183 fileMenu.addSeparator();
2184 fileMenu.add(exportImageMenu);
2185 fileMenu.add(exportFeatures);
2186 fileMenu.add(exportAnnotations);
2187 fileMenu.add(loadTreeMenuItem);
2188 fileMenu.add(associatedData);
2189 fileMenu.addSeparator();
2190 fileMenu.add(closeMenuItem);
2192 pasteMenu.add(pasteNew);
2193 pasteMenu.add(pasteThis);
2194 editMenu.add(undoMenuItem);
2195 editMenu.add(redoMenuItem);
2198 editMenu.add(pasteMenu);
2199 editMenu.add(delete);
2200 editMenu.addSeparator();
2201 editMenu.add(remove2LeftMenuItem);
2202 editMenu.add(remove2RightMenuItem);
2203 editMenu.add(removeGappedColumnMenuItem);
2204 editMenu.add(removeAllGapsMenuItem);
2205 editMenu.add(removeRedundancyMenuItem);
2206 editMenu.addSeparator();
2207 // dont add these yet in the CVS build - they cannot be undone!
2208 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2209 // editMenu.add(justifyLeftMenuItem);
2210 // editMenu.add(justifyRightMenuItem);
2211 // editMenu.addSeparator();
2212 editMenu.add(padGapsMenuitem);
2214 showMenu.add(showAllColumns);
2215 showMenu.add(showAllSeqs);
2216 showMenu.add(showAllhidden);
2217 hideMenu.add(hideSelColumns);
2218 hideMenu.add(hideSelSequences);
2219 hideMenu.add(hideAllSelection);
2220 hideMenu.add(hideAllButSelection);
2221 viewMenu.add(newView);
2222 viewMenu.add(expandViews);
2223 viewMenu.add(gatherViews);
2224 viewMenu.addSeparator();
2225 viewMenu.add(showMenu);
2226 viewMenu.add(hideMenu);
2227 viewMenu.add(showComplementMenuItem);
2228 viewMenu.addSeparator();
2229 viewMenu.add(followHighlightMenuItem);
2230 viewMenu.addSeparator();
2231 viewMenu.add(showSeqFeatures);
2232 // viewMenu.add(showSeqFeaturesHeight);
2233 viewMenu.add(openFeatureSettings);
2234 tooltipSettingsMenu.add(showDbRefsMenuitem);
2235 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2236 viewMenu.add(tooltipSettingsMenu);
2237 viewMenu.addSeparator();
2238 viewMenu.add(alignmentProperties);
2239 viewMenu.addSeparator();
2240 viewMenu.add(overviewMenuItem);
2242 annotationsMenu.add(annotationPanelMenuItem);
2243 annotationsMenu.addSeparator();
2244 annotationsMenu.add(showAllAlAnnotations);
2245 annotationsMenu.add(hideAllAlAnnotations);
2246 annotationsMenu.addSeparator();
2247 annotationsMenu.add(showAllSeqAnnotations);
2248 annotationsMenu.add(hideAllSeqAnnotations);
2249 annotationsMenu.add(sortAnnBySequence);
2250 annotationsMenu.add(sortAnnByLabel);
2251 annotationsMenu.addSeparator();
2252 autoAnnMenu.add(showAutoFirst);
2253 autoAnnMenu.add(showAutoLast);
2254 autoAnnMenu.addSeparator();
2255 autoAnnMenu.add(applyAutoAnnotationSettings);
2256 autoAnnMenu.add(showConsensusHistogram);
2257 autoAnnMenu.add(showSequenceLogo);
2258 autoAnnMenu.add(normaliseSequenceLogo);
2259 autoAnnMenu.addSeparator();
2260 autoAnnMenu.add(showGroupConservation);
2261 autoAnnMenu.add(showGroupConsensus);
2262 annotationsMenu.add(autoAnnMenu);
2264 colourMenu.add(applyToAllGroups);
2265 colourMenu.add(textColour);
2266 colourMenu.addSeparator();
2267 colourMenu.add(noColourmenuItem);
2268 colourMenu.add(clustalColour);
2269 colourMenu.add(BLOSUM62Colour);
2270 colourMenu.add(PIDColour);
2271 colourMenu.add(zappoColour);
2272 colourMenu.add(taylorColour);
2273 colourMenu.add(hydrophobicityColour);
2274 colourMenu.add(helixColour);
2275 colourMenu.add(strandColour);
2276 colourMenu.add(turnColour);
2277 colourMenu.add(buriedColour);
2278 colourMenu.add(nucleotideColour);
2279 colourMenu.add(purinePyrimidineColour);
2280 colourMenu.add(RNAInteractionColour);
2281 // colourMenu.add(covariationColour);
2282 colourMenu.add(tcoffeeColour);
2283 colourMenu.add(userDefinedColour);
2284 colourMenu.addSeparator();
2285 colourMenu.add(conservationMenuItem);
2286 colourMenu.add(modifyConservation);
2287 colourMenu.add(abovePIDThreshold);
2288 colourMenu.add(modifyPID);
2289 colourMenu.add(annotationColour);
2290 colourMenu.add(rnahelicesColour);
2292 sort.add(sortIDMenuItem);
2293 sort.add(sortLengthMenuItem);
2294 sort.add(sortGroupMenuItem);
2295 sort.add(sortPairwiseMenuItem);
2296 sort.add(sortByTreeMenu);
2297 calculateMenu.add(sort);
2298 calculateMenu.add(calculateTree);
2299 calculateMenu.addSeparator();
2300 calculateMenu.add(pairwiseAlignmentMenuItem);
2301 calculateMenu.add(PCAMenuItem);
2302 calculateMenu.addSeparator();
2303 calculateMenu.add(showTranslation);
2304 calculateMenu.add(showReverse);
2305 calculateMenu.add(showReverseComplement);
2306 calculateMenu.add(showProducts);
2307 calculateMenu.add(autoCalculate);
2308 calculateMenu.add(sortByTree);
2309 calculateMenu.addSeparator();
2310 calculateMenu.add(expandAlignment);
2311 calculateMenu.add(extractScores);
2312 calculateMenu.addSeparator();
2313 calculateMenu.add(runGroovy);
2315 webServiceNoServices = new JMenuItem(
2316 MessageManager.getString("label.no_services"));
2317 webService.add(webServiceNoServices);
2318 exportImageMenu.add(htmlMenuItem);
2319 exportImageMenu.add(epsFile);
2320 exportImageMenu.add(createPNG);
2321 exportImageMenu.add(createBioJS);
2322 exportImageMenu.add(createSVG);
2323 addSequenceMenu.add(addFromFile);
2324 addSequenceMenu.add(addFromText);
2325 addSequenceMenu.add(addFromURL);
2326 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2327 statusPanel.add(statusBar, null);
2328 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2330 formatMenu.add(font);
2331 formatMenu.addSeparator();
2332 formatMenu.add(wrapMenuItem);
2333 formatMenu.add(scaleAbove);
2334 formatMenu.add(scaleLeft);
2335 formatMenu.add(scaleRight);
2336 formatMenu.add(seqLimits);
2337 formatMenu.add(idRightAlign);
2338 formatMenu.add(hiddenMarkers);
2339 formatMenu.add(viewBoxesMenuItem);
2340 formatMenu.add(viewTextMenuItem);
2341 formatMenu.add(colourTextMenuItem);
2342 formatMenu.add(renderGapsMenuItem);
2343 formatMenu.add(centreColumnLabelsMenuItem);
2344 formatMenu.add(showNonconservedMenuItem);
2345 selectMenu.add(findMenuItem);
2346 selectMenu.addSeparator();
2347 selectMenu.add(selectAllSequenceMenuItem);
2348 selectMenu.add(deselectAllSequenceMenuItem);
2349 selectMenu.add(invertSequenceMenuItem);
2350 selectMenu.add(invertColSel);
2351 selectMenu.add(createGroup);
2352 selectMenu.add(unGroup);
2353 selectMenu.add(grpsFromSelection);
2354 selectMenu.add(deleteGroups);
2355 selectMenu.add(annotationColumn);
2356 // TODO - determine if the listenToViewSelections button is needed : see bug
2358 // selectMenu.addSeparator();
2359 // selectMenu.add(listenToViewSelections);
2363 * Generate the reverse sequence (or reverse complement if the flag is true)
2364 * and add it to the alignment
2368 protected void showReverse_actionPerformed(boolean complement)
2373 * Try to run script in a Groovy console, having first ensured that this
2374 * alignframe is set as currentAlignFrame in Desktop
2376 protected void runGroovy_actionPerformed()
2381 * Adds the given action listener and key accelerator to the given menu item.
2382 * Also saves in a lookup table to support lookup of action by key stroke.
2386 * @param actionListener
2388 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2389 JMenuItem menuItem, ActionListener actionListener)
2391 menuItem.setAccelerator(keyStroke);
2392 accelerators.put(keyStroke, menuItem);
2393 menuItem.addActionListener(actionListener);
2397 * Action on clicking sort annotations by type.
2401 protected void sortAnnotations_actionPerformed()
2406 * Action on clicking Show all annotations.
2408 * @param forSequences
2409 * update sequence-related annotations
2410 * @param forAlignment
2411 * update non-sequence-related annotations
2413 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2414 boolean forAlignment)
2416 setAnnotationsVisibility(true, forSequences, forAlignment);
2420 * Action on clicking Hide all annotations.
2422 * @param forSequences
2423 * update sequence-related annotations
2424 * @param forAlignment
2425 * update non-sequence-related annotations
2427 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2428 boolean forAlignment)
2430 setAnnotationsVisibility(false, forSequences, forAlignment);
2434 * Set the visibility of annotations to true or false. Can act on
2435 * sequence-related annotations, or alignment-related, or both.
2438 * @param forSequences
2439 * update sequence-related annotations
2440 * @param forAlignment
2441 * update non-sequence-related annotations
2443 protected void setAnnotationsVisibility(boolean visible,
2444 boolean forSequences, boolean forAlignment)
2449 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2451 // TODO Auto-generated method stub
2455 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2457 // TODO Auto-generated method stub
2461 protected void showAllhidden_actionPerformed(ActionEvent e)
2463 // TODO Auto-generated method stub
2467 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2469 // TODO Auto-generated method stub
2473 protected void hideAllSelection_actionPerformed(ActionEvent e)
2475 // TODO Auto-generated method stub
2479 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2481 // TODO Auto-generated method stub
2485 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2487 // TODO Auto-generated method stub
2491 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2493 // TODO Auto-generated method stub
2497 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2499 // TODO Auto-generated method stub
2503 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2505 // TODO Auto-generated method stub
2509 protected void showGroupConservation_actionPerformed(ActionEvent e)
2511 // TODO Auto-generated method stub
2515 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2517 // TODO Auto-generated method stub
2521 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2523 // TODO Auto-generated method stub
2527 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2529 // TODO Auto-generated method stub
2533 protected void followHighlight_actionPerformed()
2535 // TODO Auto-generated method stub
2539 protected void showNpFeats_actionPerformed(ActionEvent e)
2541 // TODO Auto-generated method stub
2545 protected void showDbRefs_actionPerformed(ActionEvent e)
2547 // TODO Auto-generated method stub
2551 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2555 protected void buildSortByAnnotationScoresMenu()
2559 protected void extractScores_actionPerformed(ActionEvent e)
2563 protected void outputText_actionPerformed(ActionEvent e)
2567 public void addFromFile_actionPerformed(ActionEvent e)
2572 public void addFromText_actionPerformed(ActionEvent e)
2577 public void addFromURL_actionPerformed(ActionEvent e)
2582 public void exportFeatures_actionPerformed(ActionEvent e)
2587 public void exportAnnotations_actionPerformed(ActionEvent e)
2592 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2596 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2601 protected void closeMenuItem_actionPerformed(boolean b)
2605 protected void redoMenuItem_actionPerformed(ActionEvent e)
2609 protected void undoMenuItem_actionPerformed(ActionEvent e)
2613 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2617 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2621 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2625 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2629 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2633 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2637 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2641 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2645 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2649 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2653 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2657 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2661 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2665 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2669 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2673 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2677 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2681 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2685 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2689 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2693 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2697 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2701 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2705 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2709 protected void clustalColour_actionPerformed(ActionEvent e)
2713 protected void zappoColour_actionPerformed(ActionEvent e)
2717 protected void taylorColour_actionPerformed(ActionEvent e)
2721 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2725 protected void helixColour_actionPerformed(ActionEvent e)
2729 protected void strandColour_actionPerformed(ActionEvent e)
2733 protected void turnColour_actionPerformed(ActionEvent e)
2737 protected void buriedColour_actionPerformed(ActionEvent e)
2741 protected void userDefinedColour_actionPerformed(ActionEvent e)
2745 protected void PIDColour_actionPerformed(ActionEvent e)
2749 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2753 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2757 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2762 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2765 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2769 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2773 protected void printMenuItem_actionPerformed(ActionEvent e)
2777 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2781 protected void findMenuItem_actionPerformed(ActionEvent e)
2785 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2789 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2793 protected void nucleotideColour_actionPerformed(ActionEvent e)
2797 protected void deleteGroups_actionPerformed(ActionEvent e)
2801 protected void createGroup_actionPerformed(ActionEvent e)
2805 protected void unGroup_actionPerformed(ActionEvent e)
2809 protected void copy_actionPerformed(ActionEvent e)
2813 protected void cut_actionPerformed(ActionEvent e)
2817 protected void delete_actionPerformed(ActionEvent e)
2821 protected void pasteNew_actionPerformed(ActionEvent e)
2825 protected void pasteThis_actionPerformed(ActionEvent e)
2829 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2833 public void createPNG(java.io.File f)
2837 protected void font_actionPerformed(ActionEvent e)
2841 protected void seqLimit_actionPerformed(ActionEvent e)
2845 public void seqDBRef_actionPerformed(ActionEvent e)
2850 public void createEPS(java.io.File f)
2854 public void createSVG(java.io.File f)
2859 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2865 * Template method to handle the 'load T-Coffee scores' menu event.
2867 * Subclasses override this method to provide a custom action.
2872 protected void loadScores_actionPerformed(ActionEvent event)
2878 * Template method to handle the 'Color T-Coffee scores' menu event.
2880 * Subclasses override this method to provide a custom action.
2885 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2890 protected void jpred_actionPerformed(ActionEvent e)
2894 protected void scaleAbove_actionPerformed(ActionEvent e)
2898 protected void scaleLeft_actionPerformed(ActionEvent e)
2902 protected void scaleRight_actionPerformed(ActionEvent e)
2906 protected void modifyPID_actionPerformed(ActionEvent e)
2910 protected void modifyConservation_actionPerformed(ActionEvent e)
2914 protected void saveAs_actionPerformed(ActionEvent e)
2918 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2922 public void vamsasStore_actionPerformed(ActionEvent e)
2927 public void vamsasLoad_actionPerformed(ActionEvent e)
2932 public void showTranslation_actionPerformed(ActionEvent e)
2937 public void featureSettings_actionPerformed(ActionEvent e)
2942 public void fetchSequence_actionPerformed(ActionEvent e)
2947 public void smoothFont_actionPerformed(ActionEvent e)
2952 public void annotationColour_actionPerformed(ActionEvent e)
2957 public void annotationColumn_actionPerformed(ActionEvent e)
2962 public void rnahelicesColour_actionPerformed(ActionEvent e)
2967 public void associatedData_actionPerformed(ActionEvent e)
2972 public void autoCalculate_actionPerformed(ActionEvent e)
2977 public void sortByTreeOption_actionPerformed(ActionEvent e)
2982 public void showAllSeqs_actionPerformed(ActionEvent e)
2987 public void showAllColumns_actionPerformed(ActionEvent e)
2992 public void hideSelSequences_actionPerformed(ActionEvent e)
2997 public void hideSelColumns_actionPerformed(ActionEvent e)
3002 public void hiddenMarkers_actionPerformed(ActionEvent e)
3007 public void findPdbId_actionPerformed(ActionEvent e)
3012 public void enterPdbId_actionPerformed(ActionEvent e)
3017 public void pdbFile_actionPerformed(ActionEvent e)
3022 public void invertColSel_actionPerformed(ActionEvent e)
3027 public void tabSelectionChanged(int sel)
3032 public void tabbedPane_mousePressed(MouseEvent e)
3037 public void tabbedPane_focusGained(FocusEvent e)
3042 public void save_actionPerformed(ActionEvent e)
3047 public void reload_actionPerformed(ActionEvent e)
3052 public void newView_actionPerformed(ActionEvent e)
3057 public void textColour_actionPerformed(ActionEvent e)
3062 public void idRightAlign_actionPerformed(ActionEvent e)
3067 public void expandViews_actionPerformed(ActionEvent e)
3072 public void gatherViews_actionPerformed(ActionEvent e)
3077 public void buildTreeMenu()
3082 public void pageSetup_actionPerformed(ActionEvent e)
3087 public void alignmentProperties()
3092 protected void expand_newalign(ActionEvent e)
3094 // TODO Auto-generated method stub
3098 protected boolean isShowAutoCalculatedAbove()
3100 return showAutoCalculatedAbove;
3103 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3105 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3108 protected SequenceAnnotationOrder getAnnotationSortOrder()
3110 return annotationSortOrder;
3113 protected void setAnnotationSortOrder(
3114 SequenceAnnotationOrder annotationSortOrder)
3116 this.annotationSortOrder = annotationSortOrder;
3119 public Map<KeyStroke, JMenuItem> getAccelerators()
3121 return this.accelerators;
3125 * Returns the selected index of the tabbed pane, or -1 if none selected
3126 * (including the case where the tabbed pane has not been made visible).
3130 public int getTabIndex()
3132 return tabbedPane.getSelectedIndex();
3135 public JPanel getStatusPanel()
3141 * Sets a reference to the containing split frame. Also makes the 'toggle
3142 * split view' menu item visible and checked.
3146 public void setSplitFrame(SplitContainerI sf)
3148 this.splitFrame = sf;
3151 this.showComplementMenuItem.setVisible(true);
3152 this.showComplementMenuItem.setState(true);
3156 public SplitContainerI getSplitViewContainer()
3158 return this.splitFrame;
3161 protected void showComplement_actionPerformed(boolean complement)