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.schemes.ColourSchemeProperty;
29 import jalview.util.MessageManager;
31 import java.awt.BorderLayout;
32 import java.awt.Color;
33 import java.awt.GridLayout;
34 import java.awt.Toolkit;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.ActionListener;
37 import java.awt.event.FocusAdapter;
38 import java.awt.event.FocusEvent;
39 import java.awt.event.KeyEvent;
40 import java.awt.event.MouseAdapter;
41 import java.awt.event.MouseEvent;
42 import java.util.HashMap;
45 import javax.swing.BorderFactory;
46 import javax.swing.ButtonGroup;
47 import javax.swing.JCheckBoxMenuItem;
48 import javax.swing.JInternalFrame;
49 import javax.swing.JLabel;
50 import javax.swing.JMenu;
51 import javax.swing.JMenuBar;
52 import javax.swing.JMenuItem;
53 import javax.swing.JOptionPane;
54 import javax.swing.JPanel;
55 import javax.swing.JRadioButtonMenuItem;
56 import javax.swing.JTabbedPane;
57 import javax.swing.KeyStroke;
58 import javax.swing.event.ChangeEvent;
59 import javax.swing.event.MenuEvent;
60 import javax.swing.event.MenuListener;
62 public class GAlignFrame extends JInternalFrame
64 protected JMenuBar alignFrameMenuBar = new JMenuBar();
66 protected JMenuItem closeMenuItem = new JMenuItem();
68 protected JMenu colourMenu = new JMenu();
70 protected JMenu webService = new JMenu();
72 protected JMenuItem webServiceNoServices;
74 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
76 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
78 protected JMenu sortByAnnotScore = new JMenu();
80 public JLabel statusBar = new JLabel();
82 protected JMenu outputTextboxMenu = new JMenu();
84 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
86 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
88 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
90 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
92 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
94 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
96 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
98 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
100 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
102 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
104 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
112 // protected JRadioButtonMenuItem covariationColour = new
113 // JRadioButtonMenuItem();
115 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
117 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
119 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
121 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
123 protected JMenuItem undoMenuItem = new JMenuItem();
125 protected JMenuItem redoMenuItem = new JMenuItem();
127 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
129 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
131 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
133 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
135 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
137 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
139 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
141 JMenuItem copy = new JMenuItem();
143 JMenuItem cut = new JMenuItem();
145 JMenu pasteMenu = new JMenu();
147 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
149 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
151 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
153 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
155 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
157 protected JMenuItem modifyConservation = new JMenuItem();
159 protected JMenu sortByTreeMenu = new JMenu();
161 protected JMenu sort = new JMenu();
163 protected JMenu calculateTree = new JMenu();
165 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
167 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
169 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
171 protected ButtonGroup colours = new ButtonGroup();
173 protected JMenuItem showTranslation = new JMenuItem();
175 protected JMenuItem showReverse = new JMenuItem();
177 protected JMenuItem showReverseComplement = new JMenuItem();
179 protected JMenu showProducts = new JMenu();
181 protected JMenuItem runGroovy = new JMenuItem();
183 protected JMenuItem rnahelicesColour = new JMenuItem();
185 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
187 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
189 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
191 protected JPanel statusPanel = new JPanel();
193 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
195 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
197 protected JMenuItem showAllAlAnnotations = new JMenuItem();
199 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
201 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
203 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
205 protected JTabbedPane tabbedPane = new JTabbedPane();
207 protected JMenuItem reload = new JMenuItem();
209 protected JMenu formatMenu = new JMenu();
211 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
213 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
215 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
217 protected JMenuItem gatherViews = new JMenuItem();
219 protected JMenuItem expandViews = new JMenuItem();
221 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
223 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
225 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
227 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
229 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
231 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
233 private SequenceAnnotationOrder annotationSortOrder;
235 private boolean showAutoCalculatedAbove = false;
237 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
239 private SplitContainerI splitFrame;
246 setJMenuBar(alignFrameMenuBar);
248 // dynamically fill save as menu with available formats
249 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
251 JMenuItem item = new JMenuItem(
252 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
254 item.addActionListener(new ActionListener()
257 public void actionPerformed(ActionEvent e)
259 outputText_actionPerformed(e);
263 outputTextboxMenu.add(item);
265 } catch (Exception e)
267 System.err.println(e.toString());
270 if (!jalview.util.Platform.isAMac())
272 closeMenuItem.setMnemonic('C');
273 outputTextboxMenu.setMnemonic('T');
274 undoMenuItem.setMnemonic('Z');
275 redoMenuItem.setMnemonic('0');
276 copy.setMnemonic('C');
277 cut.setMnemonic('U');
278 pasteMenu.setMnemonic('P');
279 reload.setMnemonic('R');
282 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
284 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
285 .getUserColourSchemes().keys();
287 while (userColours.hasMoreElements())
289 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
290 userColours.nextElement().toString());
291 radioItem.setName("USER_DEFINED");
292 radioItem.addMouseListener(new MouseAdapter()
295 public void mousePressed(MouseEvent evt)
297 if (evt.isPopupTrigger())
299 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
301 int option = JOptionPane.showInternalConfirmDialog(
302 jalview.gui.Desktop.desktop,
304 .getString("label.remove_from_default_list"),
306 .getString("label.remove_user_defined_colour"),
307 JOptionPane.YES_NO_OPTION);
308 if (option == JOptionPane.YES_OPTION)
310 jalview.gui.UserDefinedColours
311 .removeColourFromDefaults(radioItem.getText());
312 colourMenu.remove(radioItem);
316 radioItem.addActionListener(new ActionListener()
319 public void actionPerformed(ActionEvent evt)
321 userDefinedColour_actionPerformed(evt);
328 radioItem.addActionListener(new ActionListener()
331 public void actionPerformed(ActionEvent evt)
333 userDefinedColour_actionPerformed(evt);
336 colourMenu.insert(radioItem, 15);
337 colours.add(radioItem);
340 colours.add(noColourmenuItem);
341 colours.add(clustalColour);
342 colours.add(zappoColour);
343 colours.add(taylorColour);
344 colours.add(hydrophobicityColour);
345 colours.add(helixColour);
346 colours.add(strandColour);
347 colours.add(turnColour);
348 colours.add(buriedColour);
349 colours.add(userDefinedColour);
350 colours.add(PIDColour);
351 colours.add(BLOSUM62Colour);
352 colours.add(nucleotideColour);
353 colours.add(purinePyrimidineColour);
354 // colours.add(covariationColour);
355 colours.add(tcoffeeColour);
356 colours.add(RNAInteractionColour);
357 setColourSelected(jalview.bin.Cache.getDefault(
358 Preferences.DEFAULT_COLOUR, "None"));
361 public void setColourSelected(String defaultColour)
364 if (defaultColour != null)
366 int index = ColourSchemeProperty
367 .getColourIndexFromName(defaultColour);
371 case ColourSchemeProperty.CLUSTAL:
372 clustalColour.setSelected(true);
376 case ColourSchemeProperty.BLOSUM:
377 BLOSUM62Colour.setSelected(true);
381 case ColourSchemeProperty.PID:
382 PIDColour.setSelected(true);
386 case ColourSchemeProperty.ZAPPO:
387 zappoColour.setSelected(true);
391 case ColourSchemeProperty.TAYLOR:
392 taylorColour.setSelected(true);
395 case ColourSchemeProperty.HYDROPHOBIC:
396 hydrophobicityColour.setSelected(true);
400 case ColourSchemeProperty.HELIX:
401 helixColour.setSelected(true);
405 case ColourSchemeProperty.STRAND:
406 strandColour.setSelected(true);
410 case ColourSchemeProperty.TURN:
411 turnColour.setSelected(true);
415 case ColourSchemeProperty.BURIED:
416 buriedColour.setSelected(true);
420 case ColourSchemeProperty.NUCLEOTIDE:
421 nucleotideColour.setSelected(true);
425 case ColourSchemeProperty.TCOFFEE:
426 tcoffeeColour.setSelected(true);
429 case ColourSchemeProperty.PURINEPYRIMIDINE:
430 purinePyrimidineColour.setSelected(true);
434 case ColourSchemeProperty.RNAINTERACTION:
435 RNAInteractionColour.setSelected(true);
439 * case ColourSchemeProperty.COVARIATION:
440 * covariationColour.setSelected(true);
444 case ColourSchemeProperty.USER_DEFINED:
445 userDefinedColour.setSelected(true);
448 case ColourSchemeProperty.NONE:
450 noColourmenuItem.setSelected(true);
458 private void jbInit() throws Exception
460 JMenuItem saveAs = new JMenuItem(
461 MessageManager.getString("action.save_as"));
462 ActionListener al = new ActionListener()
465 public void actionPerformed(ActionEvent e)
467 saveAs_actionPerformed(e);
470 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
471 .getDefaultToolkit().getMenuShortcutKeyMask()
472 | KeyEvent.SHIFT_MASK, false);
473 addMenuActionAndAccelerator(keyStroke, saveAs, al);
475 closeMenuItem.setText(MessageManager.getString("action.close"));
476 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
477 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
478 al = new ActionListener()
481 public void actionPerformed(ActionEvent e)
483 closeMenuItem_actionPerformed(false);
486 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
488 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
489 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
490 JMenu annotationsMenu = new JMenu(
491 MessageManager.getString("action.annotations"));
492 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
493 colourMenu.setText(MessageManager.getString("action.colour"));
494 JMenu calculateMenu = new JMenu(
495 MessageManager.getString("action.calculate"));
496 webService.setText(MessageManager.getString("action.web_service"));
497 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
498 MessageManager.getString("action.select_all"));
499 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
500 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
501 al = new ActionListener()
504 public void actionPerformed(ActionEvent e)
506 selectAllSequenceMenuItem_actionPerformed(e);
509 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
511 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
512 MessageManager.getString("action.deselect_all"));
513 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
514 al = new ActionListener()
517 public void actionPerformed(ActionEvent e)
519 deselectAllSequenceMenuItem_actionPerformed(e);
522 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
524 JMenuItem invertSequenceMenuItem = new JMenuItem(
525 MessageManager.getString("action.invert_sequence_selection"));
526 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
527 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
528 al = new ActionListener()
531 public void actionPerformed(ActionEvent e)
533 invertSequenceMenuItem_actionPerformed(e);
536 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
538 JMenuItem grpsFromSelection = new JMenuItem(
539 MessageManager.getString("action.make_groups_selection"));
540 grpsFromSelection.addActionListener(new ActionListener()
543 public void actionPerformed(ActionEvent e)
545 makeGrpsFromSelection_actionPerformed(e);
548 JMenuItem expandAlignment = new JMenuItem(
549 MessageManager.getString("action.view_flanking_regions"));
550 expandAlignment.setToolTipText(MessageManager
551 .getString("label.view_flanking_regions"));
552 expandAlignment.addActionListener(new ActionListener()
555 public void actionPerformed(ActionEvent e)
560 JMenuItem remove2LeftMenuItem = new JMenuItem(
561 MessageManager.getString("action.remove_left"));
562 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
563 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
564 al = new ActionListener()
567 public void actionPerformed(ActionEvent e)
569 remove2LeftMenuItem_actionPerformed(e);
572 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
574 JMenuItem remove2RightMenuItem = new JMenuItem(
575 MessageManager.getString("action.remove_right"));
576 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
577 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
578 al = new ActionListener()
581 public void actionPerformed(ActionEvent e)
583 remove2RightMenuItem_actionPerformed(e);
586 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
588 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
589 MessageManager.getString("action.remove_empty_columns"));
590 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
591 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
592 al = new ActionListener()
595 public void actionPerformed(ActionEvent e)
597 removeGappedColumnMenuItem_actionPerformed(e);
600 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
602 JMenuItem removeAllGapsMenuItem = new JMenuItem(
603 MessageManager.getString("action.remove_all_gaps"));
604 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
605 .getDefaultToolkit().getMenuShortcutKeyMask()
606 | KeyEvent.SHIFT_MASK, false);
607 al = new ActionListener()
610 public void actionPerformed(ActionEvent e)
612 removeAllGapsMenuItem_actionPerformed(e);
615 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
617 JMenuItem justifyLeftMenuItem = new JMenuItem(
618 MessageManager.getString("action.left_justify_alignment"));
619 justifyLeftMenuItem.addActionListener(new ActionListener()
622 public void actionPerformed(ActionEvent e)
624 justifyLeftMenuItem_actionPerformed(e);
627 JMenuItem justifyRightMenuItem = new JMenuItem(
628 MessageManager.getString("action.right_justify_alignment"));
629 justifyRightMenuItem.addActionListener(new ActionListener()
632 public void actionPerformed(ActionEvent e)
634 justifyRightMenuItem_actionPerformed(e);
637 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
638 viewBoxesMenuItem.setState(true);
639 viewBoxesMenuItem.addActionListener(new ActionListener()
642 public void actionPerformed(ActionEvent e)
644 viewBoxesMenuItem_actionPerformed(e);
647 viewTextMenuItem.setText(MessageManager.getString("action.text"));
648 viewTextMenuItem.setState(true);
649 viewTextMenuItem.addActionListener(new ActionListener()
652 public void actionPerformed(ActionEvent e)
654 viewTextMenuItem_actionPerformed(e);
657 showNonconservedMenuItem.setText(MessageManager
658 .getString("label.show_non_conversed"));
659 showNonconservedMenuItem.setState(false);
660 showNonconservedMenuItem.addActionListener(new ActionListener()
663 public void actionPerformed(ActionEvent e)
665 showUnconservedMenuItem_actionPerformed(e);
668 JMenuItem sortPairwiseMenuItem = new JMenuItem(
669 MessageManager.getString("action.by_pairwise_id"));
670 sortPairwiseMenuItem.addActionListener(new ActionListener()
673 public void actionPerformed(ActionEvent e)
675 sortPairwiseMenuItem_actionPerformed(e);
678 JMenuItem sortIDMenuItem = new JMenuItem(
679 MessageManager.getString("action.by_id"));
680 sortIDMenuItem.addActionListener(new ActionListener()
683 public void actionPerformed(ActionEvent e)
685 sortIDMenuItem_actionPerformed(e);
688 JMenuItem sortLengthMenuItem = new JMenuItem(
689 MessageManager.getString("action.by_length"));
690 sortLengthMenuItem.addActionListener(new ActionListener()
693 public void actionPerformed(ActionEvent e)
695 sortLengthMenuItem_actionPerformed(e);
698 JMenuItem sortGroupMenuItem = new JMenuItem(
699 MessageManager.getString("action.by_group"));
700 sortGroupMenuItem.addActionListener(new ActionListener()
703 public void actionPerformed(ActionEvent e)
705 sortGroupMenuItem_actionPerformed(e);
709 JMenuItem removeRedundancyMenuItem = new JMenuItem(
710 MessageManager.getString("action.remove_redundancy"));
711 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
712 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
713 al = new ActionListener()
716 public void actionPerformed(ActionEvent e)
718 removeRedundancyMenuItem_actionPerformed(e);
721 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
723 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
724 MessageManager.getString("action.pairwise_alignment"));
725 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
728 public void actionPerformed(ActionEvent e)
730 pairwiseAlignmentMenuItem_actionPerformed(e);
733 JMenuItem PCAMenuItem = new JMenuItem(
734 MessageManager.getString("label.principal_component_analysis"));
735 PCAMenuItem.addActionListener(new ActionListener()
738 public void actionPerformed(ActionEvent e)
740 PCAMenuItem_actionPerformed(e);
743 JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
744 MessageManager.getString("label.average_distance_identity"));
745 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
748 public void actionPerformed(ActionEvent e)
750 averageDistanceTreeMenuItem_actionPerformed(e);
753 JMenuItem neighbourTreeMenuItem = new JMenuItem(
754 MessageManager.getString("label.neighbour_joining_identity"));
755 neighbourTreeMenuItem.addActionListener(new ActionListener()
758 public void actionPerformed(ActionEvent e)
760 neighbourTreeMenuItem_actionPerformed(e);
764 this.getContentPane().setLayout(new BorderLayout());
765 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
766 statusBar.setBackground(Color.white);
767 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
768 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
769 statusBar.setText(MessageManager.getString("label.status_bar"));
770 outputTextboxMenu.setText(MessageManager
771 .getString("label.out_to_textbox"));
772 clustalColour.setText(MessageManager.getString("label.clustalx"));
773 clustalColour.addActionListener(new ActionListener()
776 public void actionPerformed(ActionEvent e)
778 clustalColour_actionPerformed(e);
781 zappoColour.setText(MessageManager.getString("label.zappo"));
782 zappoColour.addActionListener(new ActionListener()
785 public void actionPerformed(ActionEvent e)
787 zappoColour_actionPerformed(e);
790 taylorColour.setText(MessageManager.getString("label.taylor"));
791 taylorColour.addActionListener(new ActionListener()
794 public void actionPerformed(ActionEvent e)
796 taylorColour_actionPerformed(e);
799 hydrophobicityColour.setText(MessageManager
800 .getString("label.hydrophobicity"));
801 hydrophobicityColour.addActionListener(new ActionListener()
804 public void actionPerformed(ActionEvent e)
806 hydrophobicityColour_actionPerformed(e);
809 helixColour.setText(MessageManager.getString("label.helix_propensity"));
810 helixColour.addActionListener(new ActionListener()
813 public void actionPerformed(ActionEvent e)
815 helixColour_actionPerformed(e);
818 strandColour.setText(MessageManager
819 .getString("label.strand_propensity"));
820 strandColour.addActionListener(new ActionListener()
823 public void actionPerformed(ActionEvent e)
825 strandColour_actionPerformed(e);
828 turnColour.setText(MessageManager.getString("label.turn_propensity"));
829 turnColour.addActionListener(new ActionListener()
832 public void actionPerformed(ActionEvent e)
834 turnColour_actionPerformed(e);
837 buriedColour.setText(MessageManager.getString("label.buried_index"));
838 buriedColour.addActionListener(new ActionListener()
841 public void actionPerformed(ActionEvent e)
843 buriedColour_actionPerformed(e);
846 userDefinedColour.setText(MessageManager
847 .getString("action.user_defined"));
848 userDefinedColour.addActionListener(new ActionListener()
851 public void actionPerformed(ActionEvent e)
853 userDefinedColour_actionPerformed(e);
857 .setText(MessageManager.getString("label.percentage_identity"));
858 PIDColour.addActionListener(new ActionListener()
861 public void actionPerformed(ActionEvent e)
863 PIDColour_actionPerformed(e);
867 .setText(MessageManager.getString("label.blosum62_score"));
868 BLOSUM62Colour.addActionListener(new ActionListener()
871 public void actionPerformed(ActionEvent e)
873 BLOSUM62Colour_actionPerformed(e);
876 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
877 nucleotideColour.addActionListener(new ActionListener()
880 public void actionPerformed(ActionEvent e)
882 nucleotideColour_actionPerformed(e);
886 purinePyrimidineColour.setText(MessageManager
887 .getString("label.purine_pyrimidine"));
888 purinePyrimidineColour.addActionListener(new ActionListener()
891 public void actionPerformed(ActionEvent e)
893 purinePyrimidineColour_actionPerformed(e);
897 RNAInteractionColour.setText("RNA Interaction type");
898 RNAInteractionColour.addActionListener(new ActionListener()
901 public void actionPerformed(ActionEvent e)
903 RNAInteractionColour_actionPerformed(e);
907 * covariationColour.setText("Covariation");
908 * covariationColour.addActionListener(new ActionListener() { public void
909 * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
913 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
914 MessageManager.getString("label.average_distance_bloslum62"));
915 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
918 public void actionPerformed(ActionEvent e)
920 avTreeBlosumMenuItem_actionPerformed(e);
923 JMenuItem njTreeBlosumMenuItem = new JMenuItem(
924 MessageManager.getString("label.neighbour_blosum62"));
925 njTreeBlosumMenuItem.addActionListener(new ActionListener()
928 public void actionPerformed(ActionEvent e)
930 njTreeBlosumMenuItem_actionPerformed(e);
933 annotationPanelMenuItem.setActionCommand("");
934 annotationPanelMenuItem.setText(MessageManager
935 .getString("label.show_annotations"));
936 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
938 annotationPanelMenuItem.addActionListener(new ActionListener()
941 public void actionPerformed(ActionEvent e)
943 annotationPanelMenuItem_actionPerformed(e);
946 showAllAlAnnotations.setText(MessageManager
947 .getString("label.show_all_al_annotations"));
948 final boolean isAnnotationPanelShown = annotationPanelMenuItem
950 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
951 showAllAlAnnotations.addActionListener(new ActionListener()
954 public void actionPerformed(ActionEvent e)
956 showAllAnnotations_actionPerformed(false, true);
959 hideAllAlAnnotations.setText(MessageManager
960 .getString("label.hide_all_al_annotations"));
961 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
962 hideAllAlAnnotations.addActionListener(new ActionListener()
965 public void actionPerformed(ActionEvent e)
967 hideAllAnnotations_actionPerformed(false, true);
970 showAllSeqAnnotations.setText(MessageManager
971 .getString("label.show_all_seq_annotations"));
972 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
973 showAllSeqAnnotations.addActionListener(new ActionListener()
976 public void actionPerformed(ActionEvent e)
978 showAllAnnotations_actionPerformed(true, false);
981 hideAllSeqAnnotations.setText(MessageManager
982 .getString("label.hide_all_seq_annotations"));
983 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
984 hideAllSeqAnnotations.addActionListener(new ActionListener()
987 public void actionPerformed(ActionEvent e)
989 hideAllAnnotations_actionPerformed(true, false);
992 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
993 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
994 SequenceAnnotationOrder.NONE.name()));
995 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
996 MessageManager.getString("label.sort_annotations_by_sequence"));
997 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
998 MessageManager.getString("label.sort_annotations_by_label"));
1001 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1002 sortAnnBySequence.addActionListener(new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 boolean newState = sortAnnBySequence.getState();
1008 sortAnnByLabel.setSelected(false);
1009 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1010 : SequenceAnnotationOrder.NONE);
1011 sortAnnotations_actionPerformed();
1015 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1016 sortAnnByLabel.addActionListener(new ActionListener()
1019 public void actionPerformed(ActionEvent e)
1021 boolean newState = sortAnnByLabel.getState();
1022 sortAnnBySequence.setSelected(false);
1023 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1024 : SequenceAnnotationOrder.NONE);
1025 sortAnnotations_actionPerformed();
1028 colourTextMenuItem.setText(MessageManager
1029 .getString("label.colour_text"));
1030 colourTextMenuItem.addActionListener(new ActionListener()
1033 public void actionPerformed(ActionEvent e)
1035 colourTextMenuItem_actionPerformed(e);
1039 JMenuItem htmlMenuItem = new JMenuItem(
1040 MessageManager.getString("label.html"));
1041 htmlMenuItem.addActionListener(new ActionListener()
1044 public void actionPerformed(ActionEvent e)
1046 htmlMenuItem_actionPerformed(e);
1050 JMenuItem createBioJS = new JMenuItem(
1051 MessageManager.getString("label.biojs_html_export"));
1052 createBioJS.addActionListener(new java.awt.event.ActionListener()
1055 public void actionPerformed(ActionEvent e)
1057 bioJSMenuItem_actionPerformed(e);
1061 JMenuItem overviewMenuItem = new JMenuItem(
1062 MessageManager.getString("label.overview_window"));
1063 overviewMenuItem.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 overviewMenuItem_actionPerformed(e);
1072 undoMenuItem.setEnabled(false);
1073 undoMenuItem.setText(MessageManager.getString("action.undo"));
1074 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
1075 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1076 al = new ActionListener()
1079 public void actionPerformed(ActionEvent e)
1081 undoMenuItem_actionPerformed(e);
1084 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
1086 redoMenuItem.setEnabled(false);
1087 redoMenuItem.setText(MessageManager.getString("action.redo"));
1088 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
1089 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1090 al = new ActionListener()
1093 public void actionPerformed(ActionEvent e)
1095 redoMenuItem_actionPerformed(e);
1098 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
1100 conservationMenuItem.setText(MessageManager
1101 .getString("action.by_conservation"));
1102 conservationMenuItem.addActionListener(new ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 conservationMenuItem_actionPerformed(e);
1110 noColourmenuItem.setText(MessageManager.getString("label.none"));
1111 noColourmenuItem.addActionListener(new ActionListener()
1114 public void actionPerformed(ActionEvent e)
1116 noColourmenuItem_actionPerformed(e);
1119 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1120 wrapMenuItem.addActionListener(new ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 wrapMenuItem_actionPerformed(e);
1129 JMenuItem printMenuItem = new JMenuItem(
1130 MessageManager.getString("action.print"));
1131 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
1132 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1133 al = new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 printMenuItem_actionPerformed(e);
1141 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
1144 .setText(MessageManager.getString("action.show_gaps"));
1145 renderGapsMenuItem.setState(true);
1146 renderGapsMenuItem.addActionListener(new ActionListener()
1149 public void actionPerformed(ActionEvent e)
1151 renderGapsMenuItem_actionPerformed(e);
1155 JMenuItem findMenuItem = new JMenuItem(
1156 MessageManager.getString("action.find"));
1157 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
1158 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1159 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1160 MessageManager.getString("label.find_tip")));
1161 al = new ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 findMenuItem_actionPerformed(e);
1169 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
1171 abovePIDThreshold.setText(MessageManager
1172 .getString("label.above_identity_threshold"));
1173 abovePIDThreshold.addActionListener(new ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 abovePIDThreshold_actionPerformed(e);
1181 showSeqFeatures.setText(MessageManager
1182 .getString("label.show_sequence_features"));
1183 showSeqFeatures.addActionListener(new ActionListener()
1186 public void actionPerformed(ActionEvent actionEvent)
1188 showSeqFeatures_actionPerformed(actionEvent);
1192 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1193 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1194 * void actionPerformed(ActionEvent actionEvent) {
1195 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1197 showDbRefsMenuitem.setText(MessageManager
1198 .getString("label.show_database_refs"));
1199 showDbRefsMenuitem.addActionListener(new ActionListener()
1203 public void actionPerformed(ActionEvent e)
1205 showDbRefs_actionPerformed(e);
1209 showNpFeatsMenuitem.setText(MessageManager
1210 .getString("label.show_non_positional_features"));
1211 showNpFeatsMenuitem.addActionListener(new ActionListener()
1215 public void actionPerformed(ActionEvent e)
1217 showNpFeats_actionPerformed(e);
1221 showGroupConservation.setText(MessageManager
1222 .getString("label.group_conservation"));
1223 showGroupConservation.addActionListener(new ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 showGroupConservation_actionPerformed(e);
1234 showGroupConsensus.setText(MessageManager
1235 .getString("label.group_consensus"));
1236 showGroupConsensus.addActionListener(new ActionListener()
1240 public void actionPerformed(ActionEvent e)
1242 showGroupConsensus_actionPerformed(e);
1246 showConsensusHistogram.setText(MessageManager
1247 .getString("label.show_consensus_histogram"));
1248 showConsensusHistogram.addActionListener(new ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 showConsensusHistogram_actionPerformed(e);
1258 showSequenceLogo.setText(MessageManager
1259 .getString("label.show_consensus_logo"));
1260 showSequenceLogo.addActionListener(new ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 showSequenceLogo_actionPerformed(e);
1270 normaliseSequenceLogo.setText(MessageManager
1271 .getString("label.norm_consensus_logo"));
1272 normaliseSequenceLogo.addActionListener(new ActionListener()
1276 public void actionPerformed(ActionEvent e)
1278 normaliseSequenceLogo_actionPerformed(e);
1282 applyAutoAnnotationSettings.setText(MessageManager
1283 .getString("label.apply_all_groups"));
1284 applyAutoAnnotationSettings.setState(false);
1285 applyAutoAnnotationSettings.setVisible(true);
1286 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 applyAutoAnnotationSettings_actionPerformed(e);
1295 ButtonGroup buttonGroup = new ButtonGroup();
1296 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
1297 MessageManager.getString("label.show_first"));
1298 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
1299 MessageManager.getString("label.show_last"));
1300 buttonGroup.add(showAutoFirst);
1301 buttonGroup.add(showAutoLast);
1302 final boolean autoFirst = Cache.getDefault(
1303 Preferences.SHOW_AUTOCALC_ABOVE, false);
1304 showAutoFirst.setSelected(autoFirst);
1305 setShowAutoCalculatedAbove(autoFirst);
1306 showAutoFirst.addActionListener(new ActionListener()
1309 public void actionPerformed(ActionEvent e)
1311 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1312 sortAnnotations_actionPerformed();
1315 showAutoLast.setSelected(!showAutoFirst.isSelected());
1316 showAutoLast.addActionListener(new ActionListener()
1319 public void actionPerformed(ActionEvent e)
1321 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1322 sortAnnotations_actionPerformed();
1326 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1327 nucleotideColour.addActionListener(new ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 nucleotideColour_actionPerformed(e);
1336 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1337 tcoffeeColour.setEnabled(false);
1338 tcoffeeColour.addActionListener(new ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 tcoffeeColorScheme_actionPerformed(e);
1348 JMenuItem deleteGroups = new JMenuItem(
1349 MessageManager.getString("action.undefine_groups"));
1350 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1351 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1352 al = new ActionListener()
1355 public void actionPerformed(ActionEvent e)
1357 deleteGroups_actionPerformed(e);
1360 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1362 JMenuItem createGroup = new JMenuItem(
1363 MessageManager.getString("action.create_groups"));
1364 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1365 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1366 al = new ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 createGroup_actionPerformed(e);
1374 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1376 JMenuItem unGroup = new JMenuItem(
1377 MessageManager.getString("action.remove_group"));
1378 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1379 .getDefaultToolkit().getMenuShortcutKeyMask()
1380 | KeyEvent.SHIFT_MASK, false);
1381 al = new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 unGroup_actionPerformed(e);
1389 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1391 copy.setText(MessageManager.getString("action.copy"));
1392 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1393 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1395 al = new ActionListener()
1398 public void actionPerformed(ActionEvent e)
1400 copy_actionPerformed(e);
1403 addMenuActionAndAccelerator(keyStroke, copy, al);
1405 cut.setText(MessageManager.getString("action.cut"));
1406 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1407 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1408 al = new ActionListener()
1411 public void actionPerformed(ActionEvent e)
1413 cut_actionPerformed(e);
1416 addMenuActionAndAccelerator(keyStroke, cut, al);
1418 JMenuItem delete = new JMenuItem(
1419 MessageManager.getString("action.delete"));
1420 delete.addActionListener(new ActionListener()
1423 public void actionPerformed(ActionEvent e)
1425 delete_actionPerformed(e);
1429 pasteMenu.setText(MessageManager.getString("action.paste"));
1430 JMenuItem pasteNew = new JMenuItem(
1431 MessageManager.getString("label.to_new_alignment"));
1432 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1433 .getDefaultToolkit().getMenuShortcutKeyMask()
1434 | KeyEvent.SHIFT_MASK, false);
1435 al = new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1440 pasteNew_actionPerformed(e);
1443 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1445 JMenuItem pasteThis = new JMenuItem(
1446 MessageManager.getString("label.to_this_alignment"));
1447 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1448 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1449 al = new ActionListener()
1452 public void actionPerformed(ActionEvent e)
1454 pasteThis_actionPerformed(e);
1457 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1459 applyToAllGroups.setText(MessageManager
1460 .getString("label.apply_colour_to_all_groups"));
1461 applyToAllGroups.addActionListener(new ActionListener()
1464 public void actionPerformed(ActionEvent e)
1466 applyToAllGroups_actionPerformed(e);
1469 JMenuItem createPNG = new JMenuItem("PNG");
1470 createPNG.addActionListener(new ActionListener()
1473 public void actionPerformed(ActionEvent e)
1478 createPNG.setActionCommand(MessageManager
1479 .getString("label.save_png_image"));
1481 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1482 font.addActionListener(new ActionListener()
1485 public void actionPerformed(ActionEvent e)
1487 font_actionPerformed(e);
1490 seqLimits.setText(MessageManager
1491 .getString("label.show_sequence_limits"));
1492 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1493 seqLimits.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent e)
1498 seqLimit_actionPerformed(e);
1501 JMenuItem epsFile = new JMenuItem("EPS");
1502 epsFile.addActionListener(new ActionListener()
1505 public void actionPerformed(ActionEvent e)
1511 JMenuItem createSVG = new JMenuItem("SVG");
1512 createSVG.addActionListener(new ActionListener()
1515 public void actionPerformed(ActionEvent e)
1521 JMenuItem loadTreeMenuItem = new JMenuItem(
1522 MessageManager.getString("label.load_associated_tree"));
1523 loadTreeMenuItem.setActionCommand(MessageManager
1524 .getString("label.load_tree_for_sequence_set"));
1525 loadTreeMenuItem.addActionListener(new ActionListener()
1528 public void actionPerformed(ActionEvent e)
1530 loadTreeMenuItem_actionPerformed(e);
1534 scaleAbove.setVisible(false);
1535 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1536 scaleAbove.addActionListener(new ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 scaleAbove_actionPerformed(e);
1544 scaleLeft.setVisible(false);
1545 scaleLeft.setSelected(true);
1546 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1547 scaleLeft.addActionListener(new ActionListener()
1550 public void actionPerformed(ActionEvent e)
1552 scaleLeft_actionPerformed(e);
1555 scaleRight.setVisible(false);
1556 scaleRight.setSelected(true);
1557 scaleRight.setText(MessageManager.getString("action.scale_right"));
1558 scaleRight.addActionListener(new ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 scaleRight_actionPerformed(e);
1566 centreColumnLabelsMenuItem.setVisible(true);
1567 centreColumnLabelsMenuItem.setState(false);
1568 centreColumnLabelsMenuItem.setText(MessageManager
1569 .getString("label.centre_column_labels"));
1570 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1573 public void actionPerformed(ActionEvent e)
1575 centreColumnLabels_actionPerformed(e);
1578 followHighlightMenuItem.setVisible(true);
1579 followHighlightMenuItem.setState(true);
1580 followHighlightMenuItem.setText(MessageManager
1581 .getString("label.automatic_scrolling"));
1582 followHighlightMenuItem.addActionListener(new ActionListener()
1586 public void actionPerformed(ActionEvent e)
1588 followHighlight_actionPerformed();
1593 JMenuItem modifyPID = new JMenuItem(
1594 MessageManager.getString("label.modify_identity_thereshold"));
1595 modifyPID.addActionListener(new ActionListener()
1598 public void actionPerformed(ActionEvent e)
1600 modifyPID_actionPerformed(e);
1603 modifyConservation.setText(MessageManager
1604 .getString("label.modify_conservation_thereshold"));
1605 modifyConservation.addActionListener(new ActionListener()
1608 public void actionPerformed(ActionEvent e)
1610 modifyConservation_actionPerformed(e);
1614 .setText(MessageManager.getString("action.by_tree_order"));
1615 sort.setText(MessageManager.getString("action.sort"));
1616 sort.addMenuListener(new MenuListener()
1619 public void menuSelected(MenuEvent e)
1625 public void menuDeselected(MenuEvent e)
1630 public void menuCanceled(MenuEvent e)
1634 sortByAnnotScore.setText(MessageManager
1635 .getString("label.sort_by_score"));
1636 sort.add(sortByAnnotScore);
1637 sort.addMenuListener(new javax.swing.event.MenuListener()
1641 public void menuCanceled(MenuEvent e)
1646 public void menuDeselected(MenuEvent e)
1651 public void menuSelected(MenuEvent e)
1653 buildSortByAnnotationScoresMenu();
1656 sortByAnnotScore.setVisible(false);
1659 .setText(MessageManager.getString("action.calculate_tree"));
1661 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1662 padGapsMenuitem.setState(jalview.bin.Cache
1663 .getDefault("PAD_GAPS", false));
1664 padGapsMenuitem.addActionListener(new ActionListener()
1667 public void actionPerformed(ActionEvent e)
1669 padGapsMenuitem_actionPerformed(e);
1672 JMenuItem vamsasStore = new JMenuItem(
1673 MessageManager.getString("label.vamsas_store"));
1674 vamsasStore.setVisible(false);
1675 vamsasStore.addActionListener(new ActionListener()
1678 public void actionPerformed(ActionEvent e)
1680 vamsasStore_actionPerformed(e);
1683 showTranslation.setText(MessageManager
1684 .getString("label.translate_cDNA"));
1685 showTranslation.addActionListener(new ActionListener()
1688 public void actionPerformed(ActionEvent e)
1690 showTranslation_actionPerformed(e);
1693 showReverse.setText(MessageManager.getString("label.reverse"));
1694 showReverse.addActionListener(new ActionListener()
1697 public void actionPerformed(ActionEvent e)
1699 showReverse_actionPerformed(false);
1702 showReverseComplement.setText(MessageManager
1703 .getString("label.reverse_complement"));
1704 showReverseComplement.addActionListener(new ActionListener()
1707 public void actionPerformed(ActionEvent e)
1709 showReverse_actionPerformed(true);
1713 JMenuItem extractScores = new JMenuItem(
1714 MessageManager.getString("label.extract_scores"));
1715 extractScores.addActionListener(new ActionListener()
1718 public void actionPerformed(ActionEvent e)
1720 extractScores_actionPerformed(e);
1723 extractScores.setVisible(true);
1724 // JBPNote: TODO: make gui for regex based score extraction
1726 // for show products actions see AlignFrame.canShowProducts
1727 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1729 runGroovy.setText(MessageManager.getString("label.run_groovy"));
1730 runGroovy.setToolTipText(MessageManager.getString("label.run_groovy_tip"));
1731 runGroovy.addActionListener(new ActionListener()
1734 public void actionPerformed(ActionEvent e)
1736 runGroovy_actionPerformed();
1740 JMenuItem openFeatureSettings = new JMenuItem(
1741 MessageManager.getString("action.feature_settings"));
1742 openFeatureSettings.addActionListener(new ActionListener()
1745 public void actionPerformed(ActionEvent e)
1747 featureSettings_actionPerformed(e);
1750 JMenuItem fetchSequence = new JMenuItem(
1751 MessageManager.getString("label.fetch_sequences"));
1752 fetchSequence.addActionListener(new ActionListener()
1755 public void actionPerformed(ActionEvent e)
1757 fetchSequence_actionPerformed(e);
1761 JMenuItem annotationColour = new JMenuItem(
1762 MessageManager.getString("action.by_annotation"));
1763 annotationColour.addActionListener(new ActionListener()
1766 public void actionPerformed(ActionEvent e)
1768 annotationColour_actionPerformed(e);
1772 JMenuItem annotationColumn = new JMenuItem(
1773 MessageManager.getString("action.select_by_annotation"));
1774 annotationColumn.addActionListener(new ActionListener()
1777 public void actionPerformed(ActionEvent e)
1779 annotationColumn_actionPerformed(e);
1783 rnahelicesColour.setText(MessageManager
1784 .getString("action.by_rna_helixes"));
1785 rnahelicesColour.addActionListener(new ActionListener()
1788 public void actionPerformed(ActionEvent e)
1790 rnahelicesColour_actionPerformed(e);
1794 JMenuItem associatedData = new JMenuItem(
1795 MessageManager.getString("label.load_features_annotations"));
1796 associatedData.addActionListener(new ActionListener()
1799 public void actionPerformed(ActionEvent e)
1801 associatedData_actionPerformed(e);
1804 autoCalculate.setText(MessageManager
1805 .getString("label.autocalculate_consensus"));
1806 autoCalculate.setState(jalview.bin.Cache.getDefault(
1807 "AUTO_CALC_CONSENSUS", true));
1808 autoCalculate.addActionListener(new ActionListener()
1811 public void actionPerformed(ActionEvent e)
1813 autoCalculate_actionPerformed(e);
1816 sortByTree.setText(MessageManager
1817 .getString("label.sort_alignment_new_tree"));
1819 .setToolTipText("<html>"
1821 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1823 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1824 sortByTree.addActionListener(new ActionListener()
1827 public void actionPerformed(ActionEvent e)
1829 sortByTreeOption_actionPerformed(e);
1833 listenToViewSelections.setText(MessageManager
1834 .getString("label.listen_for_selections"));
1835 listenToViewSelections
1836 .setToolTipText("<html>"
1838 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1839 listenToViewSelections.setState(false);
1840 listenToViewSelections.addActionListener(new ActionListener()
1843 public void actionPerformed(ActionEvent e)
1845 listenToViewSelections_actionPerformed(e);
1849 JMenu addSequenceMenu = new JMenu(
1850 MessageManager.getString("label.add_sequences"));
1851 JMenuItem addFromFile = new JMenuItem(
1852 MessageManager.getString("label.from_file"));
1853 addFromFile.addActionListener(new ActionListener()
1856 public void actionPerformed(ActionEvent e)
1858 addFromFile_actionPerformed(e);
1861 JMenuItem addFromText = new JMenuItem(
1862 MessageManager.getString("label.from_textbox"));
1863 addFromText.addActionListener(new ActionListener()
1866 public void actionPerformed(ActionEvent e)
1868 addFromText_actionPerformed(e);
1871 JMenuItem addFromURL = new JMenuItem(
1872 MessageManager.getString("label.from_url"));
1873 addFromURL.addActionListener(new ActionListener()
1876 public void actionPerformed(ActionEvent e)
1878 addFromURL_actionPerformed(e);
1881 JMenuItem exportFeatures = new JMenuItem(
1882 MessageManager.getString("label.export_features"));
1883 exportFeatures.addActionListener(new ActionListener()
1886 public void actionPerformed(ActionEvent e)
1888 exportFeatures_actionPerformed(e);
1891 JMenuItem exportAnnotations = new JMenuItem(
1892 MessageManager.getString("label.export_annotations"));
1893 exportAnnotations.addActionListener(new ActionListener()
1896 public void actionPerformed(ActionEvent e)
1898 exportAnnotations_actionPerformed(e);
1901 statusPanel.setLayout(new GridLayout());
1902 JMenuItem showAllSeqs = new JMenuItem(
1903 MessageManager.getString("label.all_sequences"));
1904 showAllSeqs.setToolTipText(MessageManager
1905 .getString("label.toggle_sequence_visibility"));
1906 showAllSeqs.addActionListener(new ActionListener()
1909 public void actionPerformed(ActionEvent e)
1911 showAllSeqs_actionPerformed(e);
1914 JMenuItem showAllColumns = new JMenuItem(
1915 MessageManager.getString("label.all_columns"));
1916 showAllColumns.setToolTipText(MessageManager
1917 .getString("label.toggle_columns_visibility"));
1918 showAllColumns.addActionListener(new ActionListener()
1921 public void actionPerformed(ActionEvent e)
1923 showAllColumns_actionPerformed(e);
1926 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1927 JMenuItem hideSelSequences = new JMenuItem(
1928 MessageManager.getString("label.selected_sequences"));
1929 hideSelSequences.setToolTipText(MessageManager
1930 .getString("label.toggle_sequence_visibility"));
1931 hideSelSequences.addActionListener(new ActionListener()
1934 public void actionPerformed(ActionEvent e)
1936 hideSelSequences_actionPerformed(e);
1939 JMenuItem hideSelColumns = new JMenuItem(
1940 MessageManager.getString("label.selected_columns"));
1941 hideSelColumns.setToolTipText(MessageManager
1942 .getString("label.toggle_columns_visibility"));
1943 hideSelColumns.addActionListener(new ActionListener()
1946 public void actionPerformed(ActionEvent e)
1948 hideSelColumns_actionPerformed(e);
1951 JMenuItem hideAllSelection = new JMenuItem(
1952 MessageManager.getString("label.selected_region"));
1953 hideAllSelection.addActionListener(new ActionListener()
1956 public void actionPerformed(ActionEvent e)
1958 hideAllSelection_actionPerformed(e);
1961 // TODO: should be hidden if no selection exists.
1962 JMenuItem hideAllButSelection = new JMenuItem(
1963 MessageManager.getString("label.all_but_selected_region"));
1964 hideAllButSelection.addActionListener(new ActionListener()
1967 public void actionPerformed(ActionEvent e)
1969 hideAllButSelection_actionPerformed(e);
1972 JMenuItem showAllhidden = new JMenuItem(
1973 MessageManager.getString("label.all_sequences_columns"));
1974 showAllhidden.setToolTipText(MessageManager
1975 .getString("label.toggles_visibility_hidden_selected_regions"));
1976 showAllhidden.addActionListener(new ActionListener()
1979 public void actionPerformed(ActionEvent e)
1981 showAllhidden_actionPerformed(e);
1984 hiddenMarkers.setText(MessageManager
1985 .getString("action.show_hidden_markers"));
1986 hiddenMarkers.addActionListener(new ActionListener()
1989 public void actionPerformed(ActionEvent e)
1991 hiddenMarkers_actionPerformed(e);
1995 JMenuItem invertColSel = new JMenuItem(
1996 MessageManager.getString("action.invert_column_selection"));
1997 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1998 .getDefaultToolkit().getMenuShortcutKeyMask()
1999 | KeyEvent.ALT_MASK, false);
2000 al = new ActionListener()
2003 public void actionPerformed(ActionEvent e)
2005 invertColSel_actionPerformed(e);
2008 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
2010 showComplementMenuItem.setVisible(false);
2011 showComplementMenuItem.addActionListener(new ActionListener()
2014 public void actionPerformed(ActionEvent e)
2016 showComplement_actionPerformed(showComplementMenuItem.getState());
2020 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2023 public void stateChanged(ChangeEvent evt)
2025 JTabbedPane pane = (JTabbedPane) evt.getSource();
2026 int sel = pane.getSelectedIndex();
2027 tabSelectionChanged(sel);
2030 tabbedPane.addMouseListener(new MouseAdapter()
2033 public void mousePressed(MouseEvent e)
2035 tabbedPane_mousePressed(e);
2038 tabbedPane.addFocusListener(new FocusAdapter()
2041 public void focusGained(FocusEvent e)
2043 tabbedPane_focusGained(e);
2047 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
2048 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
2049 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2050 al = new ActionListener()
2053 public void actionPerformed(ActionEvent e)
2055 save_actionPerformed(e);
2058 addMenuActionAndAccelerator(keyStroke, save, al);
2060 reload.setEnabled(false);
2061 reload.setText(MessageManager.getString("action.reload"));
2062 reload.addActionListener(new ActionListener()
2065 public void actionPerformed(ActionEvent e)
2067 reload_actionPerformed(e);
2071 JMenuItem newView = new JMenuItem(
2072 MessageManager.getString("action.new_view"));
2073 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
2074 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2075 al = new ActionListener()
2078 public void actionPerformed(ActionEvent e)
2080 newView_actionPerformed(e);
2083 addMenuActionAndAccelerator(keyStroke, newView, al);
2085 tabbedPane.setToolTipText("<html><i>"
2086 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2088 JMenuItem textColour = new JMenuItem(
2089 MessageManager.getString("action.set_text_colour"));
2090 textColour.addActionListener(new ActionListener()
2093 public void actionPerformed(ActionEvent e)
2095 textColour_actionPerformed(e);
2098 formatMenu.setText(MessageManager.getString("action.format"));
2099 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
2100 idRightAlign.setText(MessageManager
2101 .getString("label.right_align_sequence_id"));
2102 idRightAlign.addActionListener(new ActionListener()
2105 public void actionPerformed(ActionEvent e)
2107 idRightAlign_actionPerformed(e);
2111 gatherViews.setEnabled(false);
2112 gatherViews.setText(MessageManager.getString("action.gather_views"));
2113 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
2114 al = new ActionListener()
2117 public void actionPerformed(ActionEvent e)
2119 gatherViews_actionPerformed(e);
2122 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
2124 expandViews.setEnabled(false);
2125 expandViews.setText(MessageManager.getString("action.expand_views"));
2126 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
2127 al = new ActionListener()
2130 public void actionPerformed(ActionEvent e)
2132 expandViews_actionPerformed(e);
2135 addMenuActionAndAccelerator(keyStroke, expandViews, al);
2137 JMenuItem pageSetup = new JMenuItem(
2138 MessageManager.getString("action.page_setup"));
2139 pageSetup.addActionListener(new ActionListener()
2142 public void actionPerformed(ActionEvent e)
2144 pageSetup_actionPerformed(e);
2147 JMenuItem alignmentProperties = new JMenuItem(
2148 MessageManager.getString("label.alignment_props"));
2149 alignmentProperties.addActionListener(new ActionListener()
2152 public void actionPerformed(ActionEvent actionEvent)
2154 alignmentProperties();
2157 JMenu tooltipSettingsMenu = new JMenu(
2158 MessageManager.getString("label.sequence_id_tooltip"));
2159 JMenu autoAnnMenu = new JMenu(
2160 MessageManager.getString("label.autocalculated_annotation"));
2162 JMenu exportImageMenu = new JMenu(
2163 MessageManager.getString("label.export_image"));
2164 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
2165 alignFrameMenuBar.add(fileMenu);
2166 alignFrameMenuBar.add(editMenu);
2167 alignFrameMenuBar.add(selectMenu);
2168 alignFrameMenuBar.add(viewMenu);
2169 alignFrameMenuBar.add(annotationsMenu);
2170 alignFrameMenuBar.add(formatMenu);
2171 alignFrameMenuBar.add(colourMenu);
2172 alignFrameMenuBar.add(calculateMenu);
2173 alignFrameMenuBar.add(webService);
2175 fileMenu.add(fetchSequence);
2176 fileMenu.add(addSequenceMenu);
2177 fileMenu.add(reload);
2178 fileMenu.addSeparator();
2179 fileMenu.add(vamsasStore);
2181 fileMenu.add(saveAs);
2182 fileMenu.add(outputTextboxMenu);
2183 fileMenu.add(pageSetup);
2184 fileMenu.add(printMenuItem);
2185 fileMenu.addSeparator();
2186 fileMenu.add(exportImageMenu);
2187 fileMenu.add(exportFeatures);
2188 fileMenu.add(exportAnnotations);
2189 fileMenu.add(loadTreeMenuItem);
2190 fileMenu.add(associatedData);
2191 fileMenu.addSeparator();
2192 fileMenu.add(closeMenuItem);
2194 pasteMenu.add(pasteNew);
2195 pasteMenu.add(pasteThis);
2196 editMenu.add(undoMenuItem);
2197 editMenu.add(redoMenuItem);
2200 editMenu.add(pasteMenu);
2201 editMenu.add(delete);
2202 editMenu.addSeparator();
2203 editMenu.add(remove2LeftMenuItem);
2204 editMenu.add(remove2RightMenuItem);
2205 editMenu.add(removeGappedColumnMenuItem);
2206 editMenu.add(removeAllGapsMenuItem);
2207 editMenu.add(removeRedundancyMenuItem);
2208 editMenu.addSeparator();
2209 // dont add these yet in the CVS build - they cannot be undone!
2210 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2211 // editMenu.add(justifyLeftMenuItem);
2212 // editMenu.add(justifyRightMenuItem);
2213 // editMenu.addSeparator();
2214 editMenu.add(padGapsMenuitem);
2216 showMenu.add(showAllColumns);
2217 showMenu.add(showAllSeqs);
2218 showMenu.add(showAllhidden);
2219 hideMenu.add(hideSelColumns);
2220 hideMenu.add(hideSelSequences);
2221 hideMenu.add(hideAllSelection);
2222 hideMenu.add(hideAllButSelection);
2223 viewMenu.add(newView);
2224 viewMenu.add(expandViews);
2225 viewMenu.add(gatherViews);
2226 viewMenu.addSeparator();
2227 viewMenu.add(showMenu);
2228 viewMenu.add(hideMenu);
2229 viewMenu.add(showComplementMenuItem);
2230 viewMenu.addSeparator();
2231 viewMenu.add(followHighlightMenuItem);
2232 viewMenu.addSeparator();
2233 viewMenu.add(showSeqFeatures);
2234 // viewMenu.add(showSeqFeaturesHeight);
2235 viewMenu.add(openFeatureSettings);
2236 tooltipSettingsMenu.add(showDbRefsMenuitem);
2237 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2238 viewMenu.add(tooltipSettingsMenu);
2239 viewMenu.addSeparator();
2240 viewMenu.add(alignmentProperties);
2241 viewMenu.addSeparator();
2242 viewMenu.add(overviewMenuItem);
2244 annotationsMenu.add(annotationPanelMenuItem);
2245 annotationsMenu.addSeparator();
2246 annotationsMenu.add(showAllAlAnnotations);
2247 annotationsMenu.add(hideAllAlAnnotations);
2248 annotationsMenu.addSeparator();
2249 annotationsMenu.add(showAllSeqAnnotations);
2250 annotationsMenu.add(hideAllSeqAnnotations);
2251 annotationsMenu.add(sortAnnBySequence);
2252 annotationsMenu.add(sortAnnByLabel);
2253 annotationsMenu.addSeparator();
2254 autoAnnMenu.add(showAutoFirst);
2255 autoAnnMenu.add(showAutoLast);
2256 autoAnnMenu.addSeparator();
2257 autoAnnMenu.add(applyAutoAnnotationSettings);
2258 autoAnnMenu.add(showConsensusHistogram);
2259 autoAnnMenu.add(showSequenceLogo);
2260 autoAnnMenu.add(normaliseSequenceLogo);
2261 autoAnnMenu.addSeparator();
2262 autoAnnMenu.add(showGroupConservation);
2263 autoAnnMenu.add(showGroupConsensus);
2264 annotationsMenu.add(autoAnnMenu);
2266 colourMenu.add(applyToAllGroups);
2267 colourMenu.add(textColour);
2268 colourMenu.addSeparator();
2269 colourMenu.add(noColourmenuItem);
2270 colourMenu.add(clustalColour);
2271 colourMenu.add(BLOSUM62Colour);
2272 colourMenu.add(PIDColour);
2273 colourMenu.add(zappoColour);
2274 colourMenu.add(taylorColour);
2275 colourMenu.add(hydrophobicityColour);
2276 colourMenu.add(helixColour);
2277 colourMenu.add(strandColour);
2278 colourMenu.add(turnColour);
2279 colourMenu.add(buriedColour);
2280 colourMenu.add(nucleotideColour);
2281 colourMenu.add(purinePyrimidineColour);
2282 colourMenu.add(RNAInteractionColour);
2283 // colourMenu.add(covariationColour);
2284 colourMenu.add(tcoffeeColour);
2285 colourMenu.add(userDefinedColour);
2286 colourMenu.addSeparator();
2287 colourMenu.add(conservationMenuItem);
2288 colourMenu.add(modifyConservation);
2289 colourMenu.add(abovePIDThreshold);
2290 colourMenu.add(modifyPID);
2291 colourMenu.add(annotationColour);
2292 colourMenu.add(rnahelicesColour);
2294 sort.add(sortIDMenuItem);
2295 sort.add(sortLengthMenuItem);
2296 sort.add(sortGroupMenuItem);
2297 sort.add(sortPairwiseMenuItem);
2298 sort.add(sortByTreeMenu);
2299 calculateMenu.add(sort);
2300 calculateMenu.add(calculateTree);
2301 calculateMenu.addSeparator();
2302 calculateMenu.add(pairwiseAlignmentMenuItem);
2303 calculateMenu.add(PCAMenuItem);
2304 calculateMenu.addSeparator();
2305 calculateMenu.add(showTranslation);
2306 calculateMenu.add(showReverse);
2307 calculateMenu.add(showReverseComplement);
2308 calculateMenu.add(showProducts);
2309 calculateMenu.add(autoCalculate);
2310 calculateMenu.add(sortByTree);
2311 calculateMenu.addSeparator();
2312 calculateMenu.add(expandAlignment);
2313 calculateMenu.add(extractScores);
2314 calculateMenu.addSeparator();
2315 calculateMenu.add(runGroovy);
2317 webServiceNoServices = new JMenuItem(
2318 MessageManager.getString("label.no_services"));
2319 webService.add(webServiceNoServices);
2320 exportImageMenu.add(htmlMenuItem);
2321 exportImageMenu.add(epsFile);
2322 exportImageMenu.add(createPNG);
2323 exportImageMenu.add(createBioJS);
2324 exportImageMenu.add(createSVG);
2325 addSequenceMenu.add(addFromFile);
2326 addSequenceMenu.add(addFromText);
2327 addSequenceMenu.add(addFromURL);
2328 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2329 statusPanel.add(statusBar, null);
2330 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2332 formatMenu.add(font);
2333 formatMenu.addSeparator();
2334 formatMenu.add(wrapMenuItem);
2335 formatMenu.add(scaleAbove);
2336 formatMenu.add(scaleLeft);
2337 formatMenu.add(scaleRight);
2338 formatMenu.add(seqLimits);
2339 formatMenu.add(idRightAlign);
2340 formatMenu.add(hiddenMarkers);
2341 formatMenu.add(viewBoxesMenuItem);
2342 formatMenu.add(viewTextMenuItem);
2343 formatMenu.add(colourTextMenuItem);
2344 formatMenu.add(renderGapsMenuItem);
2345 formatMenu.add(centreColumnLabelsMenuItem);
2346 formatMenu.add(showNonconservedMenuItem);
2347 selectMenu.add(findMenuItem);
2348 selectMenu.addSeparator();
2349 selectMenu.add(selectAllSequenceMenuItem);
2350 selectMenu.add(deselectAllSequenceMenuItem);
2351 selectMenu.add(invertSequenceMenuItem);
2352 selectMenu.add(invertColSel);
2353 selectMenu.add(createGroup);
2354 selectMenu.add(unGroup);
2355 selectMenu.add(grpsFromSelection);
2356 selectMenu.add(deleteGroups);
2357 selectMenu.add(annotationColumn);
2358 // TODO - determine if the listenToViewSelections button is needed : see bug
2360 // selectMenu.addSeparator();
2361 // selectMenu.add(listenToViewSelections);
2365 * Generate the reverse sequence (or reverse complement if the flag is true)
2366 * and add it to the alignment
2370 protected void showReverse_actionPerformed(boolean complement)
2375 * Try to run script in a Groovy console, having first ensured that this
2376 * alignframe is set as currentAlignFrame in Desktop
2378 protected void runGroovy_actionPerformed()
2383 * Adds the given action listener and key accelerator to the given menu item.
2384 * Also saves in a lookup table to support lookup of action by key stroke.
2388 * @param actionListener
2390 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2391 JMenuItem menuItem, ActionListener actionListener)
2393 menuItem.setAccelerator(keyStroke);
2394 accelerators.put(keyStroke, menuItem);
2395 menuItem.addActionListener(actionListener);
2399 * Action on clicking sort annotations by type.
2403 protected void sortAnnotations_actionPerformed()
2408 * Action on clicking Show all annotations.
2410 * @param forSequences
2411 * update sequence-related annotations
2412 * @param forAlignment
2413 * update non-sequence-related annotations
2415 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2416 boolean forAlignment)
2418 setAnnotationsVisibility(true, forSequences, forAlignment);
2422 * Action on clicking Hide all annotations.
2424 * @param forSequences
2425 * update sequence-related annotations
2426 * @param forAlignment
2427 * update non-sequence-related annotations
2429 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2430 boolean forAlignment)
2432 setAnnotationsVisibility(false, forSequences, forAlignment);
2436 * Set the visibility of annotations to true or false. Can act on
2437 * sequence-related annotations, or alignment-related, or both.
2440 * @param forSequences
2441 * update sequence-related annotations
2442 * @param forAlignment
2443 * update non-sequence-related annotations
2445 protected void setAnnotationsVisibility(boolean visible,
2446 boolean forSequences, boolean forAlignment)
2451 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2453 // TODO Auto-generated method stub
2457 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2459 // TODO Auto-generated method stub
2463 protected void showAllhidden_actionPerformed(ActionEvent e)
2465 // TODO Auto-generated method stub
2469 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2471 // TODO Auto-generated method stub
2475 protected void hideAllSelection_actionPerformed(ActionEvent e)
2477 // TODO Auto-generated method stub
2481 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2483 // TODO Auto-generated method stub
2487 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2489 // TODO Auto-generated method stub
2493 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2495 // TODO Auto-generated method stub
2499 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2501 // TODO Auto-generated method stub
2505 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2507 // TODO Auto-generated method stub
2511 protected void showGroupConservation_actionPerformed(ActionEvent e)
2513 // TODO Auto-generated method stub
2517 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2519 // TODO Auto-generated method stub
2523 protected void showSeqFeaturesHeight_actionPerformed(
2524 ActionEvent actionEvent)
2526 // TODO Auto-generated method stub
2530 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2532 // TODO Auto-generated method stub
2536 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2538 // TODO Auto-generated method stub
2542 protected void followHighlight_actionPerformed()
2544 // TODO Auto-generated method stub
2548 protected void showNpFeats_actionPerformed(ActionEvent e)
2550 // TODO Auto-generated method stub
2554 protected void showDbRefs_actionPerformed(ActionEvent e)
2556 // TODO Auto-generated method stub
2560 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2564 protected void buildSortByAnnotationScoresMenu()
2568 protected void extractScores_actionPerformed(ActionEvent e)
2572 protected void outputText_actionPerformed(ActionEvent e)
2576 public void addFromFile_actionPerformed(ActionEvent e)
2581 public void addFromText_actionPerformed(ActionEvent e)
2586 public void addFromURL_actionPerformed(ActionEvent e)
2591 public void exportFeatures_actionPerformed(ActionEvent e)
2596 public void exportAnnotations_actionPerformed(ActionEvent e)
2601 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2605 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2610 protected void closeMenuItem_actionPerformed(boolean b)
2614 protected void redoMenuItem_actionPerformed(ActionEvent e)
2618 protected void undoMenuItem_actionPerformed(ActionEvent e)
2622 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2626 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2630 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2634 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2638 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2642 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2646 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2650 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2654 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2658 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2662 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2666 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2670 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2674 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2678 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2682 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2686 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2690 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2694 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2698 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2702 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2706 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2710 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2714 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2718 protected void clustalColour_actionPerformed(ActionEvent e)
2722 protected void zappoColour_actionPerformed(ActionEvent e)
2726 protected void taylorColour_actionPerformed(ActionEvent e)
2730 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2734 protected void helixColour_actionPerformed(ActionEvent e)
2738 protected void strandColour_actionPerformed(ActionEvent e)
2742 protected void turnColour_actionPerformed(ActionEvent e)
2746 protected void buriedColour_actionPerformed(ActionEvent e)
2750 protected void userDefinedColour_actionPerformed(ActionEvent e)
2754 protected void PIDColour_actionPerformed(ActionEvent e)
2758 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2762 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2766 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2771 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2774 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2778 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2782 protected void printMenuItem_actionPerformed(ActionEvent e)
2786 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2790 protected void findMenuItem_actionPerformed(ActionEvent e)
2794 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2798 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2802 protected void nucleotideColour_actionPerformed(ActionEvent e)
2806 protected void deleteGroups_actionPerformed(ActionEvent e)
2810 protected void createGroup_actionPerformed(ActionEvent e)
2814 protected void unGroup_actionPerformed(ActionEvent e)
2818 protected void copy_actionPerformed(ActionEvent e)
2822 protected void cut_actionPerformed(ActionEvent e)
2826 protected void delete_actionPerformed(ActionEvent e)
2830 protected void pasteNew_actionPerformed(ActionEvent e)
2834 protected void pasteThis_actionPerformed(ActionEvent e)
2838 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2842 public void createPNG(java.io.File f)
2846 protected void font_actionPerformed(ActionEvent e)
2850 protected void seqLimit_actionPerformed(ActionEvent e)
2854 public void seqDBRef_actionPerformed(ActionEvent e)
2859 public void createEPS(java.io.File f)
2863 public void createSVG(java.io.File f)
2868 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2874 * Template method to handle the 'load T-Coffee scores' menu event.
2876 * Subclasses override this method to provide a custom action.
2881 protected void loadScores_actionPerformed(ActionEvent event)
2887 * Template method to handle the 'Color T-Coffee scores' menu event.
2889 * Subclasses override this method to provide a custom action.
2894 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2899 protected void jpred_actionPerformed(ActionEvent e)
2903 protected void scaleAbove_actionPerformed(ActionEvent e)
2907 protected void scaleLeft_actionPerformed(ActionEvent e)
2911 protected void scaleRight_actionPerformed(ActionEvent e)
2915 protected void modifyPID_actionPerformed(ActionEvent e)
2919 protected void modifyConservation_actionPerformed(ActionEvent e)
2923 protected void saveAs_actionPerformed(ActionEvent e)
2927 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2931 public void vamsasStore_actionPerformed(ActionEvent e)
2936 public void vamsasLoad_actionPerformed(ActionEvent e)
2941 public void showTranslation_actionPerformed(ActionEvent e)
2946 public void featureSettings_actionPerformed(ActionEvent e)
2951 public void fetchSequence_actionPerformed(ActionEvent e)
2956 public void smoothFont_actionPerformed(ActionEvent e)
2961 public void annotationColour_actionPerformed(ActionEvent e)
2966 public void annotationColumn_actionPerformed(ActionEvent e)
2971 public void rnahelicesColour_actionPerformed(ActionEvent e)
2976 public void associatedData_actionPerformed(ActionEvent e)
2981 public void autoCalculate_actionPerformed(ActionEvent e)
2986 public void sortByTreeOption_actionPerformed(ActionEvent e)
2991 public void showAllSeqs_actionPerformed(ActionEvent e)
2996 public void showAllColumns_actionPerformed(ActionEvent e)
3001 public void hideSelSequences_actionPerformed(ActionEvent e)
3006 public void hideSelColumns_actionPerformed(ActionEvent e)
3011 public void hiddenMarkers_actionPerformed(ActionEvent e)
3016 public void findPdbId_actionPerformed(ActionEvent e)
3021 public void enterPdbId_actionPerformed(ActionEvent e)
3026 public void pdbFile_actionPerformed(ActionEvent e)
3031 public void invertColSel_actionPerformed(ActionEvent e)
3036 public void tabSelectionChanged(int sel)
3041 public void tabbedPane_mousePressed(MouseEvent e)
3046 public void tabbedPane_focusGained(FocusEvent e)
3051 public void save_actionPerformed(ActionEvent e)
3056 public void reload_actionPerformed(ActionEvent e)
3061 public void newView_actionPerformed(ActionEvent e)
3066 public void textColour_actionPerformed(ActionEvent e)
3071 public void idRightAlign_actionPerformed(ActionEvent e)
3076 public void expandViews_actionPerformed(ActionEvent e)
3081 public void gatherViews_actionPerformed(ActionEvent e)
3086 public void buildTreeMenu()
3091 public void pageSetup_actionPerformed(ActionEvent e)
3096 public void alignmentProperties()
3101 protected void expand_newalign(ActionEvent e)
3103 // TODO Auto-generated method stub
3107 protected boolean isShowAutoCalculatedAbove()
3109 return showAutoCalculatedAbove;
3112 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3114 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3117 protected SequenceAnnotationOrder getAnnotationSortOrder()
3119 return annotationSortOrder;
3122 protected void setAnnotationSortOrder(
3123 SequenceAnnotationOrder annotationSortOrder)
3125 this.annotationSortOrder = annotationSortOrder;
3128 public Map<KeyStroke, JMenuItem> getAccelerators()
3130 return this.accelerators;
3134 * Returns the selected index of the tabbed pane, or -1 if none selected
3135 * (including the case where the tabbed pane has not been made visible).
3139 public int getTabIndex()
3141 return tabbedPane.getSelectedIndex();
3144 public JPanel getStatusPanel()
3150 * Sets a reference to the containing split frame. Also makes the 'toggle
3151 * split view' menu item visible and checked.
3155 public void setSplitFrame(SplitContainerI sf)
3157 this.splitFrame = sf;
3160 this.showComplementMenuItem.setVisible(true);
3161 this.showComplementMenuItem.setState(true);
3165 public SplitContainerI getSplitViewContainer()
3167 return this.splitFrame;
3170 protected void showComplement_actionPerformed(boolean complement)