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.SwingUtilities;
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 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
142 JMenuItem copy = new JMenuItem();
144 JMenuItem cut = new JMenuItem();
146 JMenu pasteMenu = new JMenu();
148 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
152 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
154 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
156 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
158 protected JMenuItem modifyConservation = new JMenuItem();
160 protected JMenu sortByTreeMenu = new JMenu();
162 protected JMenu sort = new JMenu();
164 protected JMenu calculateTree = new JMenu();
166 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
168 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
170 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
172 protected ButtonGroup colours = new ButtonGroup();
174 protected JMenuItem showTranslation = new JMenuItem();
176 protected JMenu showProducts = new JMenu();
178 protected JMenuItem rnahelicesColour = new JMenuItem();
180 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
182 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
184 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
186 protected JPanel statusPanel = new JPanel();
188 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
190 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
192 protected JMenuItem showAllAlAnnotations = new JMenuItem();
194 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
196 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
198 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
200 protected JTabbedPane tabbedPane = new JTabbedPane();
202 protected JMenuItem reload = new JMenuItem();
204 protected JMenu formatMenu = new JMenu();
206 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
208 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
210 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
212 protected JMenuItem gatherViews = new JMenuItem();
214 protected JMenuItem expandViews = new JMenuItem();
216 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
218 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
220 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
222 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
224 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
226 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
228 private SequenceAnnotationOrder annotationSortOrder;
230 private boolean showAutoCalculatedAbove = false;
232 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
234 private SplitContainerI splitFrame;
241 setJMenuBar(alignFrameMenuBar);
243 // dynamically fill save as menu with available formats
244 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
246 JMenuItem item = new JMenuItem(
247 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
249 item.addActionListener(new ActionListener()
252 public void actionPerformed(ActionEvent e)
254 outputText_actionPerformed(e);
258 outputTextboxMenu.add(item);
260 } catch (Exception e)
262 System.err.println(e.toString());
265 if (!jalview.util.Platform.isAMac())
267 closeMenuItem.setMnemonic('C');
268 outputTextboxMenu.setMnemonic('T');
269 undoMenuItem.setMnemonic('Z');
270 redoMenuItem.setMnemonic('0');
271 copy.setMnemonic('C');
272 cut.setMnemonic('U');
273 pasteMenu.setMnemonic('P');
274 reload.setMnemonic('R');
277 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
279 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
280 .getUserColourSchemes().keys();
282 while (userColours.hasMoreElements())
284 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
285 userColours.nextElement().toString());
286 radioItem.setName("USER_DEFINED");
287 radioItem.addMouseListener(new MouseAdapter()
290 public void mousePressed(MouseEvent evt)
292 if (evt.isControlDown()
293 || SwingUtilities.isRightMouseButton(evt))
295 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
297 int option = JOptionPane.showInternalConfirmDialog(
298 jalview.gui.Desktop.desktop,
300 .getString("label.remove_from_default_list"),
302 .getString("label.remove_user_defined_colour"),
303 JOptionPane.YES_NO_OPTION);
304 if (option == JOptionPane.YES_OPTION)
306 jalview.gui.UserDefinedColours
307 .removeColourFromDefaults(radioItem.getText());
308 colourMenu.remove(radioItem);
312 radioItem.addActionListener(new ActionListener()
315 public void actionPerformed(ActionEvent evt)
317 userDefinedColour_actionPerformed(evt);
324 radioItem.addActionListener(new ActionListener()
327 public void actionPerformed(ActionEvent evt)
329 userDefinedColour_actionPerformed(evt);
332 colourMenu.insert(radioItem, 15);
333 colours.add(radioItem);
336 colours.add(noColourmenuItem);
337 colours.add(clustalColour);
338 colours.add(zappoColour);
339 colours.add(taylorColour);
340 colours.add(hydrophobicityColour);
341 colours.add(helixColour);
342 colours.add(strandColour);
343 colours.add(turnColour);
344 colours.add(buriedColour);
345 colours.add(userDefinedColour);
346 colours.add(PIDColour);
347 colours.add(BLOSUM62Colour);
348 colours.add(nucleotideColour);
349 colours.add(purinePyrimidineColour);
350 // colours.add(covariationColour);
351 colours.add(tcoffeeColour);
352 colours.add(RNAInteractionColour);
353 setColourSelected(jalview.bin.Cache.getDefault(
354 Preferences.DEFAULT_COLOUR, "None"));
357 public void setColourSelected(String defaultColour)
360 if (defaultColour != null)
362 int index = ColourSchemeProperty
363 .getColourIndexFromName(defaultColour);
367 case ColourSchemeProperty.CLUSTAL:
368 clustalColour.setSelected(true);
372 case ColourSchemeProperty.BLOSUM:
373 BLOSUM62Colour.setSelected(true);
377 case ColourSchemeProperty.PID:
378 PIDColour.setSelected(true);
382 case ColourSchemeProperty.ZAPPO:
383 zappoColour.setSelected(true);
387 case ColourSchemeProperty.TAYLOR:
388 taylorColour.setSelected(true);
391 case ColourSchemeProperty.HYDROPHOBIC:
392 hydrophobicityColour.setSelected(true);
396 case ColourSchemeProperty.HELIX:
397 helixColour.setSelected(true);
401 case ColourSchemeProperty.STRAND:
402 strandColour.setSelected(true);
406 case ColourSchemeProperty.TURN:
407 turnColour.setSelected(true);
411 case ColourSchemeProperty.BURIED:
412 buriedColour.setSelected(true);
416 case ColourSchemeProperty.NUCLEOTIDE:
417 nucleotideColour.setSelected(true);
421 case ColourSchemeProperty.TCOFFEE:
422 tcoffeeColour.setSelected(true);
425 case ColourSchemeProperty.PURINEPYRIMIDINE:
426 purinePyrimidineColour.setSelected(true);
430 case ColourSchemeProperty.RNAINTERACTION:
431 RNAInteractionColour.setSelected(true);
435 * case ColourSchemeProperty.COVARIATION:
436 * covariationColour.setSelected(true);
440 case ColourSchemeProperty.USER_DEFINED:
441 userDefinedColour.setSelected(true);
444 case ColourSchemeProperty.NONE:
446 noColourmenuItem.setSelected(true);
454 private void jbInit() throws Exception
456 JMenuItem saveAs = new JMenuItem(
457 MessageManager.getString("action.save_as"));
458 ActionListener al = new ActionListener()
461 public void actionPerformed(ActionEvent e)
463 saveAs_actionPerformed(e);
466 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
467 .getDefaultToolkit().getMenuShortcutKeyMask()
468 | KeyEvent.SHIFT_MASK, false);
469 addMenuActionAndAccelerator(keyStroke, saveAs, al);
471 closeMenuItem.setText(MessageManager.getString("action.close"));
472 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
473 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
474 al = new ActionListener()
477 public void actionPerformed(ActionEvent e)
479 closeMenuItem_actionPerformed(false);
482 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
484 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
485 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
486 JMenu annotationsMenu = new JMenu(
487 MessageManager.getString("action.annotations"));
488 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
489 colourMenu.setText(MessageManager.getString("action.colour"));
490 JMenu calculateMenu = new JMenu(
491 MessageManager.getString("action.calculate"));
492 webService.setText(MessageManager.getString("action.web_service"));
493 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
494 MessageManager.getString("action.select_all"));
495 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
496 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
497 al = new ActionListener()
500 public void actionPerformed(ActionEvent e)
502 selectAllSequenceMenuItem_actionPerformed(e);
505 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
507 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
508 MessageManager.getString("action.deselect_all"));
509 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
510 al = new ActionListener()
513 public void actionPerformed(ActionEvent e)
515 deselectAllSequenceMenuItem_actionPerformed(e);
518 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
520 JMenuItem invertSequenceMenuItem = new JMenuItem(
521 MessageManager.getString("action.invert_sequence_selection"));
522 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
523 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
524 al = new ActionListener()
527 public void actionPerformed(ActionEvent e)
529 invertSequenceMenuItem_actionPerformed(e);
532 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
534 JMenuItem grpsFromSelection = new JMenuItem(
535 MessageManager.getString("action.make_groups_selection"));
536 grpsFromSelection.addActionListener(new ActionListener()
539 public void actionPerformed(ActionEvent e)
541 makeGrpsFromSelection_actionPerformed(e);
544 JMenuItem expandAlignment = new JMenuItem(
545 MessageManager.getString("action.view_flanking_regions"));
546 expandAlignment.setToolTipText(MessageManager
547 .getString("label.view_flanking_regions"));
548 expandAlignment.addActionListener(new ActionListener()
551 public void actionPerformed(ActionEvent e)
556 JMenuItem remove2LeftMenuItem = new JMenuItem(
557 MessageManager.getString("action.remove_left"));
558 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
559 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
560 al = new ActionListener()
563 public void actionPerformed(ActionEvent e)
565 remove2LeftMenuItem_actionPerformed(e);
568 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
570 JMenuItem remove2RightMenuItem = new JMenuItem(
571 MessageManager.getString("action.remove_right"));
572 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
573 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
574 al = new ActionListener()
577 public void actionPerformed(ActionEvent e)
579 remove2RightMenuItem_actionPerformed(e);
582 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
584 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
585 MessageManager.getString("action.remove_empty_columns"));
586 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
587 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
588 al = new ActionListener()
591 public void actionPerformed(ActionEvent e)
593 removeGappedColumnMenuItem_actionPerformed(e);
596 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
598 JMenuItem removeAllGapsMenuItem = new JMenuItem(
599 MessageManager.getString("action.remove_all_gaps"));
600 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
601 .getDefaultToolkit().getMenuShortcutKeyMask()
602 | KeyEvent.SHIFT_MASK, false);
603 al = new ActionListener()
606 public void actionPerformed(ActionEvent e)
608 removeAllGapsMenuItem_actionPerformed(e);
611 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
613 JMenuItem justifyLeftMenuItem = new JMenuItem(
614 MessageManager.getString("action.left_justify_alignment"));
615 justifyLeftMenuItem.addActionListener(new ActionListener()
618 public void actionPerformed(ActionEvent e)
620 justifyLeftMenuItem_actionPerformed(e);
623 JMenuItem justifyRightMenuItem = new JMenuItem(
624 MessageManager.getString("action.right_justify_alignment"));
625 justifyRightMenuItem.addActionListener(new ActionListener()
628 public void actionPerformed(ActionEvent e)
630 justifyRightMenuItem_actionPerformed(e);
633 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
634 viewBoxesMenuItem.setState(true);
635 viewBoxesMenuItem.addActionListener(new ActionListener()
638 public void actionPerformed(ActionEvent e)
640 viewBoxesMenuItem_actionPerformed(e);
643 viewTextMenuItem.setText(MessageManager.getString("action.text"));
644 viewTextMenuItem.setState(true);
645 viewTextMenuItem.addActionListener(new ActionListener()
648 public void actionPerformed(ActionEvent e)
650 viewTextMenuItem_actionPerformed(e);
653 showNonconservedMenuItem.setText(MessageManager
654 .getString("label.show_non_conversed"));
655 showNonconservedMenuItem.setState(false);
656 showNonconservedMenuItem.addActionListener(new ActionListener()
659 public void actionPerformed(ActionEvent e)
661 showUnconservedMenuItem_actionPerformed(e);
664 JMenuItem sortPairwiseMenuItem = new JMenuItem(
665 MessageManager.getString("action.by_pairwise_id"));
666 sortPairwiseMenuItem.addActionListener(new ActionListener()
669 public void actionPerformed(ActionEvent e)
671 sortPairwiseMenuItem_actionPerformed(e);
674 JMenuItem sortIDMenuItem = new JMenuItem(
675 MessageManager.getString("action.by_id"));
676 sortIDMenuItem.addActionListener(new ActionListener()
679 public void actionPerformed(ActionEvent e)
681 sortIDMenuItem_actionPerformed(e);
684 JMenuItem sortLengthMenuItem = new JMenuItem(
685 MessageManager.getString("action.by_length"));
686 sortLengthMenuItem.addActionListener(new ActionListener()
689 public void actionPerformed(ActionEvent e)
691 sortLengthMenuItem_actionPerformed(e);
694 JMenuItem sortGroupMenuItem = new JMenuItem(
695 MessageManager.getString("action.by_group"));
696 sortGroupMenuItem.addActionListener(new ActionListener()
699 public void actionPerformed(ActionEvent e)
701 sortGroupMenuItem_actionPerformed(e);
705 JMenuItem removeRedundancyMenuItem = new JMenuItem(
706 MessageManager.getString("action.remove_redundancy"));
707 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
708 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
709 al = new ActionListener()
712 public void actionPerformed(ActionEvent e)
714 removeRedundancyMenuItem_actionPerformed(e);
717 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
719 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
720 MessageManager.getString("action.pairwise_alignment"));
721 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
724 public void actionPerformed(ActionEvent e)
726 pairwiseAlignmentMenuItem_actionPerformed(e);
729 JMenuItem PCAMenuItem = new JMenuItem(
730 MessageManager.getString("label.principal_component_analysis"));
731 PCAMenuItem.addActionListener(new ActionListener()
734 public void actionPerformed(ActionEvent e)
736 PCAMenuItem_actionPerformed(e);
739 JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
740 MessageManager.getString("label.average_distance_identity"));
741 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
744 public void actionPerformed(ActionEvent e)
746 averageDistanceTreeMenuItem_actionPerformed(e);
749 JMenuItem neighbourTreeMenuItem = new JMenuItem(
750 MessageManager.getString("label.neighbour_joining_identity"));
751 neighbourTreeMenuItem.addActionListener(new ActionListener()
754 public void actionPerformed(ActionEvent e)
756 neighbourTreeMenuItem_actionPerformed(e);
760 this.getContentPane().setLayout(new BorderLayout());
761 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
762 statusBar.setBackground(Color.white);
763 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
764 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
765 statusBar.setText(MessageManager.getString("label.status_bar"));
766 outputTextboxMenu.setText(MessageManager
767 .getString("label.out_to_textbox"));
768 clustalColour.setText(MessageManager.getString("label.clustalx"));
769 clustalColour.addActionListener(new ActionListener()
772 public void actionPerformed(ActionEvent e)
774 clustalColour_actionPerformed(e);
777 zappoColour.setText(MessageManager.getString("label.zappo"));
778 zappoColour.addActionListener(new ActionListener()
781 public void actionPerformed(ActionEvent e)
783 zappoColour_actionPerformed(e);
786 taylorColour.setText(MessageManager.getString("label.taylor"));
787 taylorColour.addActionListener(new ActionListener()
790 public void actionPerformed(ActionEvent e)
792 taylorColour_actionPerformed(e);
795 hydrophobicityColour.setText(MessageManager
796 .getString("label.hydrophobicity"));
797 hydrophobicityColour.addActionListener(new ActionListener()
800 public void actionPerformed(ActionEvent e)
802 hydrophobicityColour_actionPerformed(e);
805 helixColour.setText(MessageManager.getString("label.helix_propensity"));
806 helixColour.addActionListener(new ActionListener()
809 public void actionPerformed(ActionEvent e)
811 helixColour_actionPerformed(e);
814 strandColour.setText(MessageManager
815 .getString("label.strand_propensity"));
816 strandColour.addActionListener(new ActionListener()
819 public void actionPerformed(ActionEvent e)
821 strandColour_actionPerformed(e);
824 turnColour.setText(MessageManager.getString("label.turn_propensity"));
825 turnColour.addActionListener(new ActionListener()
828 public void actionPerformed(ActionEvent e)
830 turnColour_actionPerformed(e);
833 buriedColour.setText(MessageManager.getString("label.buried_index"));
834 buriedColour.addActionListener(new ActionListener()
837 public void actionPerformed(ActionEvent e)
839 buriedColour_actionPerformed(e);
842 userDefinedColour.setText(MessageManager
843 .getString("action.user_defined"));
844 userDefinedColour.addActionListener(new ActionListener()
847 public void actionPerformed(ActionEvent e)
849 userDefinedColour_actionPerformed(e);
853 .setText(MessageManager.getString("label.percentage_identity"));
854 PIDColour.addActionListener(new ActionListener()
857 public void actionPerformed(ActionEvent e)
859 PIDColour_actionPerformed(e);
863 .setText(MessageManager.getString("label.blosum62_score"));
864 BLOSUM62Colour.addActionListener(new ActionListener()
867 public void actionPerformed(ActionEvent e)
869 BLOSUM62Colour_actionPerformed(e);
872 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
873 nucleotideColour.addActionListener(new ActionListener()
876 public void actionPerformed(ActionEvent e)
878 nucleotideColour_actionPerformed(e);
882 purinePyrimidineColour.setText(MessageManager
883 .getString("label.purine_pyrimidine"));
884 purinePyrimidineColour.addActionListener(new ActionListener()
887 public void actionPerformed(ActionEvent e)
889 purinePyrimidineColour_actionPerformed(e);
893 RNAInteractionColour.setText("RNA Interaction type");
894 RNAInteractionColour.addActionListener(new ActionListener()
897 public void actionPerformed(ActionEvent e)
899 RNAInteractionColour_actionPerformed(e);
903 * covariationColour.setText("Covariation");
904 * covariationColour.addActionListener(new ActionListener() { public void
905 * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
909 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
910 MessageManager.getString("label.average_distance_bloslum62"));
911 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
914 public void actionPerformed(ActionEvent e)
916 avTreeBlosumMenuItem_actionPerformed(e);
919 JMenuItem njTreeBlosumMenuItem = new JMenuItem(
920 MessageManager.getString("label.neighbour_blosum62"));
921 njTreeBlosumMenuItem.addActionListener(new ActionListener()
924 public void actionPerformed(ActionEvent e)
926 njTreeBlosumMenuItem_actionPerformed(e);
929 annotationPanelMenuItem.setActionCommand("");
930 annotationPanelMenuItem.setText(MessageManager
931 .getString("label.show_annotations"));
932 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
934 annotationPanelMenuItem.addActionListener(new ActionListener()
937 public void actionPerformed(ActionEvent e)
939 annotationPanelMenuItem_actionPerformed(e);
942 showAllAlAnnotations.setText(MessageManager
943 .getString("label.show_all_al_annotations"));
944 final boolean isAnnotationPanelShown = annotationPanelMenuItem
946 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
947 showAllAlAnnotations.addActionListener(new ActionListener()
950 public void actionPerformed(ActionEvent e)
952 showAllAnnotations_actionPerformed(false, true);
955 hideAllAlAnnotations.setText(MessageManager
956 .getString("label.hide_all_al_annotations"));
957 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
958 hideAllAlAnnotations.addActionListener(new ActionListener()
961 public void actionPerformed(ActionEvent e)
963 hideAllAnnotations_actionPerformed(false, true);
966 showAllSeqAnnotations.setText(MessageManager
967 .getString("label.show_all_seq_annotations"));
968 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
969 showAllSeqAnnotations.addActionListener(new ActionListener()
972 public void actionPerformed(ActionEvent e)
974 showAllAnnotations_actionPerformed(true, false);
977 hideAllSeqAnnotations.setText(MessageManager
978 .getString("label.hide_all_seq_annotations"));
979 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
980 hideAllSeqAnnotations.addActionListener(new ActionListener()
983 public void actionPerformed(ActionEvent e)
985 hideAllAnnotations_actionPerformed(true, false);
988 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
989 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
990 SequenceAnnotationOrder.NONE.name()));
991 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
992 MessageManager.getString("label.sort_annotations_by_sequence"));
993 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
994 MessageManager.getString("label.sort_annotations_by_label"));
997 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
998 sortAnnBySequence.addActionListener(new ActionListener()
1001 public void actionPerformed(ActionEvent e)
1003 boolean newState = sortAnnBySequence.getState();
1004 sortAnnByLabel.setSelected(false);
1005 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1006 : SequenceAnnotationOrder.NONE);
1007 sortAnnotations_actionPerformed();
1011 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1012 sortAnnByLabel.addActionListener(new ActionListener()
1015 public void actionPerformed(ActionEvent e)
1017 boolean newState = sortAnnByLabel.getState();
1018 sortAnnBySequence.setSelected(false);
1019 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1020 : SequenceAnnotationOrder.NONE);
1021 sortAnnotations_actionPerformed();
1024 colourTextMenuItem.setText(MessageManager
1025 .getString("label.colour_text"));
1026 colourTextMenuItem.addActionListener(new ActionListener()
1029 public void actionPerformed(ActionEvent e)
1031 colourTextMenuItem_actionPerformed(e);
1035 JMenuItem htmlMenuItem = new JMenuItem(
1036 MessageManager.getString("label.html"));
1037 htmlMenuItem.addActionListener(new ActionListener()
1040 public void actionPerformed(ActionEvent e)
1042 htmlMenuItem_actionPerformed(e);
1046 JMenuItem createBioJS = new JMenuItem(
1047 MessageManager.getString("label.biojs_html_export"));
1048 createBioJS.addActionListener(new java.awt.event.ActionListener()
1051 public void actionPerformed(ActionEvent e)
1053 bioJSMenuItem_actionPerformed(e);
1057 JMenuItem overviewMenuItem = new JMenuItem(
1058 MessageManager.getString("label.overview_window"));
1059 overviewMenuItem.addActionListener(new ActionListener()
1062 public void actionPerformed(ActionEvent e)
1064 overviewMenuItem_actionPerformed(e);
1068 undoMenuItem.setEnabled(false);
1069 undoMenuItem.setText(MessageManager.getString("action.undo"));
1070 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
1071 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1072 al = new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 undoMenuItem_actionPerformed(e);
1080 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
1082 redoMenuItem.setEnabled(false);
1083 redoMenuItem.setText(MessageManager.getString("action.redo"));
1084 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
1085 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1086 al = new ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 redoMenuItem_actionPerformed(e);
1094 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
1096 conservationMenuItem.setText(MessageManager
1097 .getString("action.by_conservation"));
1098 conservationMenuItem.addActionListener(new ActionListener()
1101 public void actionPerformed(ActionEvent e)
1103 conservationMenuItem_actionPerformed(e);
1106 noColourmenuItem.setText(MessageManager.getString("label.none"));
1107 noColourmenuItem.addActionListener(new ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 noColourmenuItem_actionPerformed(e);
1115 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1116 wrapMenuItem.addActionListener(new ActionListener()
1119 public void actionPerformed(ActionEvent e)
1121 wrapMenuItem_actionPerformed(e);
1125 JMenuItem printMenuItem = new JMenuItem(
1126 MessageManager.getString("action.print"));
1127 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
1128 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1129 al = new ActionListener()
1132 public void actionPerformed(ActionEvent e)
1134 printMenuItem_actionPerformed(e);
1137 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
1140 .setText(MessageManager.getString("action.show_gaps"));
1141 renderGapsMenuItem.setState(true);
1142 renderGapsMenuItem.addActionListener(new ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 renderGapsMenuItem_actionPerformed(e);
1151 JMenuItem findMenuItem = new JMenuItem(
1152 MessageManager.getString("action.find"));
1153 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
1154 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1155 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1156 MessageManager.getString("label.find_tip")));
1157 al = new ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 findMenuItem_actionPerformed(e);
1165 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
1167 abovePIDThreshold.setText(MessageManager
1168 .getString("label.above_identity_threshold"));
1169 abovePIDThreshold.addActionListener(new ActionListener()
1172 public void actionPerformed(ActionEvent e)
1174 abovePIDThreshold_actionPerformed(e);
1177 showSeqFeatures.setText(MessageManager
1178 .getString("label.show_sequence_features"));
1179 showSeqFeatures.addActionListener(new ActionListener()
1182 public void actionPerformed(ActionEvent actionEvent)
1184 showSeqFeatures_actionPerformed(actionEvent);
1188 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1189 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1190 * void actionPerformed(ActionEvent actionEvent) {
1191 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1193 showDbRefsMenuitem.setText(MessageManager
1194 .getString("label.show_database_refs"));
1195 showDbRefsMenuitem.addActionListener(new ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 showDbRefs_actionPerformed(e);
1205 showNpFeatsMenuitem.setText(MessageManager
1206 .getString("label.show_non_positional_features"));
1207 showNpFeatsMenuitem.addActionListener(new ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 showNpFeats_actionPerformed(e);
1217 showGroupConservation.setText(MessageManager
1218 .getString("label.group_conservation"));
1219 showGroupConservation.addActionListener(new ActionListener()
1223 public void actionPerformed(ActionEvent e)
1225 showGroupConservation_actionPerformed(e);
1230 showGroupConsensus.setText(MessageManager
1231 .getString("label.group_consensus"));
1232 showGroupConsensus.addActionListener(new ActionListener()
1236 public void actionPerformed(ActionEvent e)
1238 showGroupConsensus_actionPerformed(e);
1242 showConsensusHistogram.setText(MessageManager
1243 .getString("label.show_consensus_histogram"));
1244 showConsensusHistogram.addActionListener(new ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 showConsensusHistogram_actionPerformed(e);
1254 showSequenceLogo.setText(MessageManager
1255 .getString("label.show_consensus_logo"));
1256 showSequenceLogo.addActionListener(new ActionListener()
1260 public void actionPerformed(ActionEvent e)
1262 showSequenceLogo_actionPerformed(e);
1266 normaliseSequenceLogo.setText(MessageManager
1267 .getString("label.norm_consensus_logo"));
1268 normaliseSequenceLogo.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 normaliseSequenceLogo_actionPerformed(e);
1278 applyAutoAnnotationSettings.setText(MessageManager
1279 .getString("label.apply_all_groups"));
1280 applyAutoAnnotationSettings.setState(false);
1281 applyAutoAnnotationSettings.setVisible(true);
1282 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1285 public void actionPerformed(ActionEvent e)
1287 applyAutoAnnotationSettings_actionPerformed(e);
1291 ButtonGroup buttonGroup = new ButtonGroup();
1292 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
1293 MessageManager.getString("label.show_first"));
1294 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
1295 MessageManager.getString("label.show_last"));
1296 buttonGroup.add(showAutoFirst);
1297 buttonGroup.add(showAutoLast);
1298 showAutoFirst.setSelected(Cache.getDefault(
1299 Preferences.SHOW_AUTOCALC_ABOVE, false));
1300 showAutoFirst.addActionListener(new ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1306 sortAnnotations_actionPerformed();
1309 showAutoLast.setSelected(!showAutoFirst.isSelected());
1310 showAutoLast.addActionListener(new ActionListener()
1313 public void actionPerformed(ActionEvent e)
1315 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1316 sortAnnotations_actionPerformed();
1320 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1321 nucleotideColour.addActionListener(new ActionListener()
1324 public void actionPerformed(ActionEvent e)
1326 nucleotideColour_actionPerformed(e);
1330 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1331 tcoffeeColour.setEnabled(false);
1332 tcoffeeColour.addActionListener(new ActionListener()
1336 public void actionPerformed(ActionEvent e)
1338 tcoffeeColorScheme_actionPerformed(e);
1342 JMenuItem deleteGroups = new JMenuItem(
1343 MessageManager.getString("action.undefine_groups"));
1344 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1345 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1346 al = new ActionListener()
1349 public void actionPerformed(ActionEvent e)
1351 deleteGroups_actionPerformed(e);
1354 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1356 JMenuItem createGroup = new JMenuItem(
1357 MessageManager.getString("action.create_groups"));
1358 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1359 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1360 al = new ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 createGroup_actionPerformed(e);
1368 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1370 JMenuItem unGroup = new JMenuItem(
1371 MessageManager.getString("action.remove_group"));
1372 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1373 .getDefaultToolkit().getMenuShortcutKeyMask()
1374 | KeyEvent.SHIFT_MASK, false);
1375 al = new ActionListener()
1378 public void actionPerformed(ActionEvent e)
1380 unGroup_actionPerformed(e);
1383 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1385 copy.setText(MessageManager.getString("action.copy"));
1386 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1387 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1389 al = new ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 copy_actionPerformed(e);
1397 addMenuActionAndAccelerator(keyStroke, copy, al);
1399 cut.setText(MessageManager.getString("action.cut"));
1400 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1401 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1402 al = new ActionListener()
1405 public void actionPerformed(ActionEvent e)
1407 cut_actionPerformed(e);
1410 addMenuActionAndAccelerator(keyStroke, cut, al);
1412 JMenuItem delete = new JMenuItem(
1413 MessageManager.getString("action.delete"));
1414 delete.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent e)
1419 delete_actionPerformed(e);
1423 pasteMenu.setText(MessageManager.getString("action.paste"));
1424 JMenuItem pasteNew = new JMenuItem(
1425 MessageManager.getString("label.to_new_alignment"));
1426 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1427 .getDefaultToolkit().getMenuShortcutKeyMask()
1428 | KeyEvent.SHIFT_MASK, false);
1429 al = new ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 pasteNew_actionPerformed(e);
1437 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1439 JMenuItem pasteThis = new JMenuItem(
1440 MessageManager.getString("label.to_this_alignment"));
1441 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1442 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1443 al = new ActionListener()
1446 public void actionPerformed(ActionEvent e)
1448 pasteThis_actionPerformed(e);
1451 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1453 applyToAllGroups.setText(MessageManager
1454 .getString("label.apply_colour_to_all_groups"));
1455 applyToAllGroups.addActionListener(new ActionListener()
1458 public void actionPerformed(ActionEvent e)
1460 applyToAllGroups_actionPerformed(e);
1463 JMenuItem createPNG = new JMenuItem("PNG");
1464 createPNG.addActionListener(new ActionListener()
1467 public void actionPerformed(ActionEvent e)
1472 createPNG.setActionCommand(MessageManager
1473 .getString("label.save_png_image"));
1475 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1476 font.addActionListener(new ActionListener()
1479 public void actionPerformed(ActionEvent e)
1481 font_actionPerformed(e);
1484 seqLimits.setText(MessageManager
1485 .getString("label.show_sequence_limits"));
1486 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1487 seqLimits.addActionListener(new ActionListener()
1490 public void actionPerformed(ActionEvent e)
1492 seqLimit_actionPerformed(e);
1495 JMenuItem epsFile = new JMenuItem("EPS");
1496 epsFile.addActionListener(new ActionListener()
1499 public void actionPerformed(ActionEvent e)
1505 JMenuItem createSVG = new JMenuItem("SVG");
1506 createSVG.addActionListener(new ActionListener()
1509 public void actionPerformed(ActionEvent e)
1515 JMenuItem loadTreeMenuItem = new JMenuItem(
1516 MessageManager.getString("label.load_associated_tree"));
1517 loadTreeMenuItem.setActionCommand(MessageManager
1518 .getString("label.load_tree_for_sequence_set"));
1519 loadTreeMenuItem.addActionListener(new ActionListener()
1522 public void actionPerformed(ActionEvent e)
1524 loadTreeMenuItem_actionPerformed(e);
1528 scaleAbove.setVisible(false);
1529 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1530 scaleAbove.addActionListener(new ActionListener()
1533 public void actionPerformed(ActionEvent e)
1535 scaleAbove_actionPerformed(e);
1538 scaleLeft.setVisible(false);
1539 scaleLeft.setSelected(true);
1540 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1541 scaleLeft.addActionListener(new ActionListener()
1544 public void actionPerformed(ActionEvent e)
1546 scaleLeft_actionPerformed(e);
1549 scaleRight.setVisible(false);
1550 scaleRight.setSelected(true);
1551 scaleRight.setText(MessageManager.getString("action.scale_right"));
1552 scaleRight.addActionListener(new ActionListener()
1555 public void actionPerformed(ActionEvent e)
1557 scaleRight_actionPerformed(e);
1560 centreColumnLabelsMenuItem.setVisible(true);
1561 centreColumnLabelsMenuItem.setState(false);
1562 centreColumnLabelsMenuItem.setText(MessageManager
1563 .getString("label.centre_column_labels"));
1564 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1567 public void actionPerformed(ActionEvent e)
1569 centreColumnLabels_actionPerformed(e);
1572 followHighlightMenuItem.setVisible(true);
1573 followHighlightMenuItem.setState(true);
1574 followHighlightMenuItem.setText(MessageManager
1575 .getString("label.automatic_scrolling"));
1576 followHighlightMenuItem.addActionListener(new ActionListener()
1580 public void actionPerformed(ActionEvent e)
1582 followHighlight_actionPerformed();
1587 JMenuItem modifyPID = new JMenuItem(
1588 MessageManager.getString("label.modify_identity_thereshold"));
1589 modifyPID.addActionListener(new ActionListener()
1592 public void actionPerformed(ActionEvent e)
1594 modifyPID_actionPerformed(e);
1597 modifyConservation.setText(MessageManager
1598 .getString("label.modify_conservation_thereshold"));
1599 modifyConservation.addActionListener(new ActionListener()
1602 public void actionPerformed(ActionEvent e)
1604 modifyConservation_actionPerformed(e);
1608 .setText(MessageManager.getString("action.by_tree_order"));
1609 sort.setText(MessageManager.getString("action.sort"));
1610 sort.addMenuListener(new MenuListener()
1613 public void menuSelected(MenuEvent e)
1619 public void menuDeselected(MenuEvent e)
1624 public void menuCanceled(MenuEvent e)
1628 sortByAnnotScore.setText(MessageManager
1629 .getString("label.sort_by_score"));
1630 sort.add(sortByAnnotScore);
1631 sort.addMenuListener(new javax.swing.event.MenuListener()
1635 public void menuCanceled(MenuEvent e)
1640 public void menuDeselected(MenuEvent e)
1645 public void menuSelected(MenuEvent e)
1647 buildSortByAnnotationScoresMenu();
1650 sortByAnnotScore.setVisible(false);
1653 .setText(MessageManager.getString("action.calculate_tree"));
1655 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1656 padGapsMenuitem.setState(jalview.bin.Cache
1657 .getDefault("PAD_GAPS", false));
1658 padGapsMenuitem.addActionListener(new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 padGapsMenuitem_actionPerformed(e);
1666 JMenuItem vamsasStore = new JMenuItem(
1667 MessageManager.getString("label.vamsas_store"));
1668 vamsasStore.setVisible(false);
1669 vamsasStore.addActionListener(new ActionListener()
1672 public void actionPerformed(ActionEvent e)
1674 vamsasStore_actionPerformed(e);
1677 showTranslation.setText(MessageManager
1678 .getString("label.translate_cDNA"));
1679 showTranslation.addActionListener(new ActionListener()
1682 public void actionPerformed(ActionEvent e)
1684 showTranslation_actionPerformed(e);
1688 JMenuItem extractScores = new JMenuItem(
1689 MessageManager.getString("label.extract_scores"));
1690 extractScores.addActionListener(new ActionListener()
1693 public void actionPerformed(ActionEvent e)
1695 extractScores_actionPerformed(e);
1698 extractScores.setVisible(true);
1699 // JBPNote: TODO: make gui for regex based score extraction
1701 // for show products actions see AlignFrame.canShowProducts
1702 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1704 JMenuItem openFeatureSettings = new JMenuItem(
1705 MessageManager.getString("action.feature_settings"));
1706 openFeatureSettings.addActionListener(new ActionListener()
1709 public void actionPerformed(ActionEvent e)
1711 featureSettings_actionPerformed(e);
1714 JMenuItem fetchSequence = new JMenuItem(
1715 MessageManager.getString("label.fetch_sequences"));
1716 fetchSequence.addActionListener(new ActionListener()
1719 public void actionPerformed(ActionEvent e)
1721 fetchSequence_actionPerformed(e);
1725 JMenuItem annotationColour = new JMenuItem(
1726 MessageManager.getString("action.by_annotation"));
1727 annotationColour.addActionListener(new ActionListener()
1730 public void actionPerformed(ActionEvent e)
1732 annotationColour_actionPerformed(e);
1736 JMenuItem annotationColumn = new JMenuItem(
1737 MessageManager.getString("action.select_by_annotation"));
1738 annotationColumn.addActionListener(new ActionListener()
1741 public void actionPerformed(ActionEvent e)
1743 annotationColumn_actionPerformed(e);
1747 rnahelicesColour.setText(MessageManager
1748 .getString("action.by_rna_helixes"));
1749 rnahelicesColour.addActionListener(new ActionListener()
1752 public void actionPerformed(ActionEvent e)
1754 rnahelicesColour_actionPerformed(e);
1758 JMenuItem associatedData = new JMenuItem(
1759 MessageManager.getString("label.load_features_annotations"));
1760 associatedData.addActionListener(new ActionListener()
1763 public void actionPerformed(ActionEvent e)
1765 associatedData_actionPerformed(e);
1768 autoCalculate.setText(MessageManager
1769 .getString("label.autocalculate_consensus"));
1770 autoCalculate.setState(jalview.bin.Cache.getDefault(
1771 "AUTO_CALC_CONSENSUS", true));
1772 autoCalculate.addActionListener(new ActionListener()
1775 public void actionPerformed(ActionEvent e)
1777 autoCalculate_actionPerformed(e);
1780 sortByTree.setText(MessageManager
1781 .getString("label.sort_alignment_new_tree"));
1783 .setToolTipText("<html>"
1785 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1787 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1788 sortByTree.addActionListener(new ActionListener()
1791 public void actionPerformed(ActionEvent e)
1793 sortByTreeOption_actionPerformed(e);
1797 listenToViewSelections.setText(MessageManager
1798 .getString("label.listen_for_selections"));
1799 listenToViewSelections
1800 .setToolTipText("<html>"
1802 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1803 listenToViewSelections.setState(false);
1804 listenToViewSelections.addActionListener(new ActionListener()
1807 public void actionPerformed(ActionEvent e)
1809 listenToViewSelections_actionPerformed(e);
1813 JMenu addSequenceMenu = new JMenu(
1814 MessageManager.getString("label.add_sequences"));
1815 JMenuItem addFromFile = new JMenuItem(
1816 MessageManager.getString("label.from_file"));
1817 addFromFile.addActionListener(new ActionListener()
1820 public void actionPerformed(ActionEvent e)
1822 addFromFile_actionPerformed(e);
1825 JMenuItem addFromText = new JMenuItem(
1826 MessageManager.getString("label.from_textbox"));
1827 addFromText.addActionListener(new ActionListener()
1830 public void actionPerformed(ActionEvent e)
1832 addFromText_actionPerformed(e);
1835 JMenuItem addFromURL = new JMenuItem(
1836 MessageManager.getString("label.from_url"));
1837 addFromURL.addActionListener(new ActionListener()
1840 public void actionPerformed(ActionEvent e)
1842 addFromURL_actionPerformed(e);
1845 JMenuItem exportFeatures = new JMenuItem(
1846 MessageManager.getString("label.export_features"));
1847 exportFeatures.addActionListener(new ActionListener()
1850 public void actionPerformed(ActionEvent e)
1852 exportFeatures_actionPerformed(e);
1855 JMenuItem exportAnnotations = new JMenuItem(
1856 MessageManager.getString("label.export_annotations"));
1857 exportAnnotations.addActionListener(new ActionListener()
1860 public void actionPerformed(ActionEvent e)
1862 exportAnnotations_actionPerformed(e);
1865 statusPanel.setLayout(new GridLayout());
1866 JMenuItem showAllSeqs = new JMenuItem(
1867 MessageManager.getString("label.all_sequences"));
1868 showAllSeqs.setToolTipText(MessageManager
1869 .getString("label.toggle_sequence_visibility"));
1870 showAllSeqs.addActionListener(new ActionListener()
1873 public void actionPerformed(ActionEvent e)
1875 showAllSeqs_actionPerformed(e);
1878 JMenuItem showAllColumns = new JMenuItem(
1879 MessageManager.getString("label.all_columns"));
1880 showAllColumns.setToolTipText(MessageManager
1881 .getString("label.toggle_columns_visibility"));
1882 showAllColumns.addActionListener(new ActionListener()
1885 public void actionPerformed(ActionEvent e)
1887 showAllColumns_actionPerformed(e);
1890 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1891 JMenuItem hideSelSequences = new JMenuItem(
1892 MessageManager.getString("label.selected_sequences"));
1893 hideSelSequences.setToolTipText(MessageManager
1894 .getString("label.toggle_sequence_visibility"));
1895 hideSelSequences.addActionListener(new ActionListener()
1898 public void actionPerformed(ActionEvent e)
1900 hideSelSequences_actionPerformed(e);
1903 JMenuItem hideSelColumns = new JMenuItem(
1904 MessageManager.getString("label.selected_columns"));
1905 hideSelColumns.setToolTipText(MessageManager
1906 .getString("label.toggle_columns_visibility"));
1907 hideSelColumns.addActionListener(new ActionListener()
1910 public void actionPerformed(ActionEvent e)
1912 hideSelColumns_actionPerformed(e);
1915 JMenuItem hideAllSelection = new JMenuItem(
1916 MessageManager.getString("label.selected_region"));
1917 hideAllSelection.addActionListener(new ActionListener()
1920 public void actionPerformed(ActionEvent e)
1922 hideAllSelection_actionPerformed(e);
1925 // TODO: should be hidden if no selection exists.
1926 JMenuItem hideAllButSelection = new JMenuItem(
1927 MessageManager.getString("label.all_but_selected_region"));
1928 hideAllButSelection.addActionListener(new ActionListener()
1931 public void actionPerformed(ActionEvent e)
1933 hideAllButSelection_actionPerformed(e);
1936 JMenuItem showAllhidden = new JMenuItem(
1937 MessageManager.getString("label.all_sequences_columns"));
1938 showAllhidden.setToolTipText(MessageManager
1939 .getString("label.toggles_visibility_hidden_selected_regions"));
1940 showAllhidden.addActionListener(new ActionListener()
1943 public void actionPerformed(ActionEvent e)
1945 showAllhidden_actionPerformed(e);
1948 hiddenMarkers.setText(MessageManager
1949 .getString("action.show_hidden_markers"));
1950 hiddenMarkers.addActionListener(new ActionListener()
1953 public void actionPerformed(ActionEvent e)
1955 hiddenMarkers_actionPerformed(e);
1959 JMenuItem invertColSel = new JMenuItem(
1960 MessageManager.getString("action.invert_column_selection"));
1961 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1962 .getDefaultToolkit().getMenuShortcutKeyMask()
1963 | KeyEvent.ALT_MASK, false);
1964 al = new ActionListener()
1967 public void actionPerformed(ActionEvent e)
1969 invertColSel_actionPerformed(e);
1972 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1974 showComplementMenuItem.setVisible(false);
1975 showComplementMenuItem.addActionListener(new ActionListener()
1978 public void actionPerformed(ActionEvent e)
1980 showComplement_actionPerformed(showComplementMenuItem.getState());
1984 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1987 public void stateChanged(ChangeEvent evt)
1989 JTabbedPane pane = (JTabbedPane) evt.getSource();
1990 int sel = pane.getSelectedIndex();
1991 tabSelectionChanged(sel);
1994 tabbedPane.addMouseListener(new MouseAdapter()
1997 public void mousePressed(MouseEvent e)
1999 tabbedPane_mousePressed(e);
2002 tabbedPane.addFocusListener(new FocusAdapter()
2005 public void focusGained(FocusEvent e)
2007 tabbedPane_focusGained(e);
2011 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
2012 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
2013 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2014 al = new ActionListener()
2017 public void actionPerformed(ActionEvent e)
2019 save_actionPerformed(e);
2022 addMenuActionAndAccelerator(keyStroke, save, al);
2024 reload.setEnabled(false);
2025 reload.setText(MessageManager.getString("action.reload"));
2026 reload.addActionListener(new ActionListener()
2029 public void actionPerformed(ActionEvent e)
2031 reload_actionPerformed(e);
2035 JMenuItem newView = new JMenuItem(
2036 MessageManager.getString("action.new_view"));
2037 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
2038 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2039 al = new ActionListener()
2042 public void actionPerformed(ActionEvent e)
2044 newView_actionPerformed(e);
2047 addMenuActionAndAccelerator(keyStroke, newView, al);
2049 tabbedPane.setToolTipText("<html><i>"
2050 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2052 JMenuItem textColour = new JMenuItem(
2053 MessageManager.getString("action.set_text_colour"));
2054 textColour.addActionListener(new ActionListener()
2057 public void actionPerformed(ActionEvent e)
2059 textColour_actionPerformed(e);
2062 formatMenu.setText(MessageManager.getString("action.format"));
2063 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
2064 idRightAlign.setText(MessageManager
2065 .getString("label.right_align_sequence_id"));
2066 idRightAlign.addActionListener(new ActionListener()
2069 public void actionPerformed(ActionEvent e)
2071 idRightAlign_actionPerformed(e);
2075 gatherViews.setEnabled(false);
2076 gatherViews.setText(MessageManager.getString("action.gather_views"));
2077 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
2078 al = new ActionListener()
2081 public void actionPerformed(ActionEvent e)
2083 gatherViews_actionPerformed(e);
2086 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
2088 expandViews.setEnabled(false);
2089 expandViews.setText(MessageManager.getString("action.expand_views"));
2090 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
2091 al = new ActionListener()
2094 public void actionPerformed(ActionEvent e)
2096 expandViews_actionPerformed(e);
2099 addMenuActionAndAccelerator(keyStroke, expandViews, al);
2101 JMenuItem pageSetup = new JMenuItem(
2102 MessageManager.getString("action.page_setup"));
2103 pageSetup.addActionListener(new ActionListener()
2106 public void actionPerformed(ActionEvent e)
2108 pageSetup_actionPerformed(e);
2111 JMenuItem alignmentProperties = new JMenuItem(
2112 MessageManager.getString("label.alignment_props"));
2113 alignmentProperties.addActionListener(new ActionListener()
2116 public void actionPerformed(ActionEvent actionEvent)
2118 alignmentProperties();
2121 JMenu tooltipSettingsMenu = new JMenu(
2122 MessageManager.getString("label.sequence_id_tooltip"));
2123 JMenu autoAnnMenu = new JMenu(
2124 MessageManager.getString("label.autocalculated_annotation"));
2126 JMenu exportImageMenu = new JMenu(
2127 MessageManager.getString("label.export_image"));
2128 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
2129 alignFrameMenuBar.add(fileMenu);
2130 alignFrameMenuBar.add(editMenu);
2131 alignFrameMenuBar.add(selectMenu);
2132 alignFrameMenuBar.add(viewMenu);
2133 alignFrameMenuBar.add(annotationsMenu);
2134 alignFrameMenuBar.add(formatMenu);
2135 alignFrameMenuBar.add(colourMenu);
2136 alignFrameMenuBar.add(calculateMenu);
2137 alignFrameMenuBar.add(webService);
2138 fileMenu.add(fetchSequence);
2139 fileMenu.add(addSequenceMenu);
2140 fileMenu.add(reload);
2141 fileMenu.addSeparator();
2142 fileMenu.add(vamsasStore);
2144 fileMenu.add(saveAs);
2145 fileMenu.add(outputTextboxMenu);
2146 fileMenu.add(pageSetup);
2147 fileMenu.add(printMenuItem);
2148 fileMenu.addSeparator();
2149 fileMenu.add(exportImageMenu);
2150 fileMenu.add(exportFeatures);
2151 fileMenu.add(exportAnnotations);
2152 fileMenu.add(loadTreeMenuItem);
2153 fileMenu.add(associatedData);
2154 fileMenu.addSeparator();
2155 fileMenu.add(closeMenuItem);
2156 editMenu.add(undoMenuItem);
2157 editMenu.add(redoMenuItem);
2160 editMenu.add(pasteMenu);
2161 editMenu.add(delete);
2162 editMenu.addSeparator();
2163 editMenu.add(remove2LeftMenuItem);
2164 editMenu.add(remove2RightMenuItem);
2165 editMenu.add(removeGappedColumnMenuItem);
2166 editMenu.add(removeAllGapsMenuItem);
2167 editMenu.add(removeRedundancyMenuItem);
2168 editMenu.addSeparator();
2169 // dont add these yet in the CVS build - they cannot be undone!
2170 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2171 // editMenu.add(justifyLeftMenuItem);
2172 // editMenu.add(justifyRightMenuItem);
2173 // editMenu.addSeparator();
2174 editMenu.add(padGapsMenuitem);
2176 viewMenu.add(newView);
2177 viewMenu.add(expandViews);
2178 viewMenu.add(gatherViews);
2179 viewMenu.addSeparator();
2180 viewMenu.add(showMenu);
2181 viewMenu.add(hideMenu);
2182 viewMenu.add(showComplementMenuItem);
2183 viewMenu.addSeparator();
2184 viewMenu.add(followHighlightMenuItem);
2185 viewMenu.addSeparator();
2186 viewMenu.add(showSeqFeatures);
2187 // viewMenu.add(showSeqFeaturesHeight);
2188 viewMenu.add(openFeatureSettings);
2189 tooltipSettingsMenu.add(showDbRefsMenuitem);
2190 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2191 viewMenu.add(tooltipSettingsMenu);
2192 viewMenu.addSeparator();
2193 viewMenu.add(alignmentProperties);
2194 viewMenu.addSeparator();
2195 viewMenu.add(overviewMenuItem);
2197 annotationsMenu.add(annotationPanelMenuItem);
2198 annotationsMenu.addSeparator();
2199 annotationsMenu.add(showAllAlAnnotations);
2200 annotationsMenu.add(hideAllAlAnnotations);
2201 annotationsMenu.addSeparator();
2202 annotationsMenu.add(showAllSeqAnnotations);
2203 annotationsMenu.add(hideAllSeqAnnotations);
2204 annotationsMenu.add(sortAnnBySequence);
2205 annotationsMenu.add(sortAnnByLabel);
2206 annotationsMenu.addSeparator();
2207 autoAnnMenu.add(showAutoFirst);
2208 autoAnnMenu.add(showAutoLast);
2209 autoAnnMenu.addSeparator();
2210 autoAnnMenu.add(applyAutoAnnotationSettings);
2211 autoAnnMenu.add(showConsensusHistogram);
2212 autoAnnMenu.add(showSequenceLogo);
2213 autoAnnMenu.add(normaliseSequenceLogo);
2214 autoAnnMenu.addSeparator();
2215 autoAnnMenu.add(showGroupConservation);
2216 autoAnnMenu.add(showGroupConsensus);
2217 annotationsMenu.add(autoAnnMenu);
2219 colourMenu.add(applyToAllGroups);
2220 colourMenu.add(textColour);
2221 colourMenu.addSeparator();
2222 colourMenu.add(noColourmenuItem);
2223 colourMenu.add(clustalColour);
2224 colourMenu.add(BLOSUM62Colour);
2225 colourMenu.add(PIDColour);
2226 colourMenu.add(zappoColour);
2227 colourMenu.add(taylorColour);
2228 colourMenu.add(hydrophobicityColour);
2229 colourMenu.add(helixColour);
2230 colourMenu.add(strandColour);
2231 colourMenu.add(turnColour);
2232 colourMenu.add(buriedColour);
2233 colourMenu.add(nucleotideColour);
2234 colourMenu.add(purinePyrimidineColour);
2235 colourMenu.add(RNAInteractionColour);
2236 // colourMenu.add(covariationColour);
2237 colourMenu.add(tcoffeeColour);
2238 colourMenu.add(userDefinedColour);
2239 colourMenu.addSeparator();
2240 colourMenu.add(conservationMenuItem);
2241 colourMenu.add(modifyConservation);
2242 colourMenu.add(abovePIDThreshold);
2243 colourMenu.add(modifyPID);
2244 colourMenu.add(annotationColour);
2245 colourMenu.add(rnahelicesColour);
2246 calculateMenu.add(sort);
2247 calculateMenu.add(calculateTree);
2248 calculateMenu.addSeparator();
2249 calculateMenu.add(pairwiseAlignmentMenuItem);
2250 calculateMenu.add(PCAMenuItem);
2251 calculateMenu.addSeparator();
2252 calculateMenu.add(showTranslation);
2253 calculateMenu.add(showProducts);
2254 calculateMenu.add(autoCalculate);
2255 calculateMenu.add(sortByTree);
2256 calculateMenu.addSeparator();
2257 calculateMenu.add(extractScores);
2258 webServiceNoServices = new JMenuItem(
2259 MessageManager.getString("label.no_services"));
2260 webService.add(webServiceNoServices);
2261 pasteMenu.add(pasteNew);
2262 pasteMenu.add(pasteThis);
2263 sort.add(sortIDMenuItem);
2264 sort.add(sortLengthMenuItem);
2265 sort.add(sortGroupMenuItem);
2266 sort.add(sortPairwiseMenuItem);
2267 sort.add(sortByTreeMenu);
2268 exportImageMenu.add(htmlMenuItem);
2269 exportImageMenu.add(epsFile);
2270 exportImageMenu.add(createPNG);
2271 exportImageMenu.add(createBioJS);
2272 exportImageMenu.add(createSVG);
2273 addSequenceMenu.add(addFromFile);
2274 addSequenceMenu.add(addFromText);
2275 addSequenceMenu.add(addFromURL);
2276 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2277 statusPanel.add(statusBar, null);
2278 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2279 showMenu.add(showAllColumns);
2280 showMenu.add(showAllSeqs);
2281 showMenu.add(showAllhidden);
2282 hideMenu.add(hideSelColumns);
2283 hideMenu.add(hideSelSequences);
2284 hideMenu.add(hideAllSelection);
2285 hideMenu.add(hideAllButSelection);
2287 formatMenu.add(font);
2288 formatMenu.addSeparator();
2289 formatMenu.add(wrapMenuItem);
2290 formatMenu.add(scaleAbove);
2291 formatMenu.add(scaleLeft);
2292 formatMenu.add(scaleRight);
2293 formatMenu.add(seqLimits);
2294 formatMenu.add(idRightAlign);
2295 formatMenu.add(hiddenMarkers);
2296 formatMenu.add(viewBoxesMenuItem);
2297 formatMenu.add(viewTextMenuItem);
2298 formatMenu.add(colourTextMenuItem);
2299 formatMenu.add(renderGapsMenuItem);
2300 formatMenu.add(centreColumnLabelsMenuItem);
2301 formatMenu.add(showNonconservedMenuItem);
2302 selectMenu.add(findMenuItem);
2303 selectMenu.addSeparator();
2304 selectMenu.add(selectAllSequenceMenuItem);
2305 selectMenu.add(deselectAllSequenceMenuItem);
2306 selectMenu.add(invertSequenceMenuItem);
2307 selectMenu.add(invertColSel);
2308 selectMenu.add(createGroup);
2309 selectMenu.add(unGroup);
2310 selectMenu.add(grpsFromSelection);
2311 selectMenu.add(deleteGroups);
2312 selectMenu.add(annotationColumn);
2313 calculateMenu.add(expandAlignment);
2314 // TODO - determine if the listenToViewSelections button is needed : see bug
2316 // selectMenu.addSeparator();
2317 // selectMenu.add(listenToViewSelections);
2321 * Adds the given action listener and key accelerator to the given menu item.
2322 * Also saves in a lookup table to support lookup of action by key stroke.
2326 * @param actionListener
2328 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2329 JMenuItem menuItem, ActionListener actionListener)
2331 menuItem.setAccelerator(keyStroke);
2332 accelerators.put(keyStroke, menuItem);
2333 menuItem.addActionListener(actionListener);
2337 * Action on clicking sort annotations by type.
2341 protected void sortAnnotations_actionPerformed()
2346 * Action on clicking Show all annotations.
2348 * @param forSequences
2349 * update sequence-related annotations
2350 * @param forAlignment
2351 * update non-sequence-related annotations
2353 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2354 boolean forAlignment)
2356 setAnnotationsVisibility(true, forSequences, forAlignment);
2360 * Action on clicking Hide all annotations.
2362 * @param forSequences
2363 * update sequence-related annotations
2364 * @param forAlignment
2365 * update non-sequence-related annotations
2367 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2368 boolean forAlignment)
2370 setAnnotationsVisibility(false, forSequences, forAlignment);
2374 * Set the visibility of annotations to true or false. Can act on
2375 * sequence-related annotations, or alignment-related, or both.
2378 * @param forSequences
2379 * update sequence-related annotations
2380 * @param forAlignment
2381 * update non-sequence-related annotations
2383 protected void setAnnotationsVisibility(boolean visible,
2384 boolean forSequences, boolean forAlignment)
2389 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2391 // TODO Auto-generated method stub
2395 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2397 // TODO Auto-generated method stub
2401 protected void showAllhidden_actionPerformed(ActionEvent e)
2403 // TODO Auto-generated method stub
2407 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2409 // TODO Auto-generated method stub
2413 protected void hideAllSelection_actionPerformed(ActionEvent e)
2415 // TODO Auto-generated method stub
2419 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2421 // TODO Auto-generated method stub
2425 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2427 // TODO Auto-generated method stub
2431 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2433 // TODO Auto-generated method stub
2437 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2439 // TODO Auto-generated method stub
2443 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2445 // TODO Auto-generated method stub
2449 protected void showGroupConservation_actionPerformed(ActionEvent e)
2451 // TODO Auto-generated method stub
2455 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2457 // TODO Auto-generated method stub
2461 protected void showSeqFeaturesHeight_actionPerformed(
2462 ActionEvent actionEvent)
2464 // TODO Auto-generated method stub
2468 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2470 // TODO Auto-generated method stub
2474 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2476 // TODO Auto-generated method stub
2480 protected void followHighlight_actionPerformed()
2482 // TODO Auto-generated method stub
2486 protected void showNpFeats_actionPerformed(ActionEvent e)
2488 // TODO Auto-generated method stub
2492 protected void showDbRefs_actionPerformed(ActionEvent e)
2494 // TODO Auto-generated method stub
2498 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2502 protected void buildSortByAnnotationScoresMenu()
2506 protected void extractScores_actionPerformed(ActionEvent e)
2510 protected void outputText_actionPerformed(ActionEvent e)
2514 public void addFromFile_actionPerformed(ActionEvent e)
2519 public void addFromText_actionPerformed(ActionEvent e)
2524 public void addFromURL_actionPerformed(ActionEvent e)
2529 public void exportFeatures_actionPerformed(ActionEvent e)
2534 public void exportAnnotations_actionPerformed(ActionEvent e)
2539 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2543 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2548 protected void closeMenuItem_actionPerformed(boolean b)
2552 protected void redoMenuItem_actionPerformed(ActionEvent e)
2556 protected void undoMenuItem_actionPerformed(ActionEvent e)
2560 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2564 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2568 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2572 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2576 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2580 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2584 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2588 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2592 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2596 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2600 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2604 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2608 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2612 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2616 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2620 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2624 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2628 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2632 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2636 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2640 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2644 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2648 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2652 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2656 protected void clustalColour_actionPerformed(ActionEvent e)
2660 protected void zappoColour_actionPerformed(ActionEvent e)
2664 protected void taylorColour_actionPerformed(ActionEvent e)
2668 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2672 protected void helixColour_actionPerformed(ActionEvent e)
2676 protected void strandColour_actionPerformed(ActionEvent e)
2680 protected void turnColour_actionPerformed(ActionEvent e)
2684 protected void buriedColour_actionPerformed(ActionEvent e)
2688 protected void userDefinedColour_actionPerformed(ActionEvent e)
2692 protected void PIDColour_actionPerformed(ActionEvent e)
2696 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2700 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2704 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2709 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2712 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2716 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2720 protected void printMenuItem_actionPerformed(ActionEvent e)
2724 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2728 protected void findMenuItem_actionPerformed(ActionEvent e)
2732 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2736 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2740 protected void nucleotideColour_actionPerformed(ActionEvent e)
2744 protected void deleteGroups_actionPerformed(ActionEvent e)
2748 protected void createGroup_actionPerformed(ActionEvent e)
2752 protected void unGroup_actionPerformed(ActionEvent e)
2756 protected void copy_actionPerformed(ActionEvent e)
2760 protected void cut_actionPerformed(ActionEvent e)
2764 protected void delete_actionPerformed(ActionEvent e)
2768 protected void pasteNew_actionPerformed(ActionEvent e)
2772 protected void pasteThis_actionPerformed(ActionEvent e)
2776 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2780 public void createPNG(java.io.File f)
2784 protected void font_actionPerformed(ActionEvent e)
2788 protected void seqLimit_actionPerformed(ActionEvent e)
2792 public void seqDBRef_actionPerformed(ActionEvent e)
2797 public void createEPS(java.io.File f)
2801 public void createSVG(java.io.File f)
2806 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2812 * Template method to handle the 'load T-Coffee scores' menu event.
2814 * Subclasses override this method to provide a custom action.
2819 protected void loadScores_actionPerformed(ActionEvent event)
2825 * Template method to handle the 'Color T-Coffee scores' menu event.
2827 * Subclasses override this method to provide a custom action.
2832 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2837 protected void jpred_actionPerformed(ActionEvent e)
2841 protected void scaleAbove_actionPerformed(ActionEvent e)
2845 protected void scaleLeft_actionPerformed(ActionEvent e)
2849 protected void scaleRight_actionPerformed(ActionEvent e)
2853 protected void modifyPID_actionPerformed(ActionEvent e)
2857 protected void modifyConservation_actionPerformed(ActionEvent e)
2861 protected void saveAs_actionPerformed(ActionEvent e)
2865 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2869 public void vamsasStore_actionPerformed(ActionEvent e)
2874 public void vamsasLoad_actionPerformed(ActionEvent e)
2879 public void showTranslation_actionPerformed(ActionEvent e)
2884 public void featureSettings_actionPerformed(ActionEvent e)
2889 public void fetchSequence_actionPerformed(ActionEvent e)
2894 public void smoothFont_actionPerformed(ActionEvent e)
2899 public void annotationColour_actionPerformed(ActionEvent e)
2904 public void annotationColumn_actionPerformed(ActionEvent e)
2909 public void rnahelicesColour_actionPerformed(ActionEvent e)
2914 public void associatedData_actionPerformed(ActionEvent e)
2919 public void autoCalculate_actionPerformed(ActionEvent e)
2924 public void sortByTreeOption_actionPerformed(ActionEvent e)
2929 public void showAllSeqs_actionPerformed(ActionEvent e)
2934 public void showAllColumns_actionPerformed(ActionEvent e)
2939 public void hideSelSequences_actionPerformed(ActionEvent e)
2944 public void hideSelColumns_actionPerformed(ActionEvent e)
2949 public void hiddenMarkers_actionPerformed(ActionEvent e)
2954 public void findPdbId_actionPerformed(ActionEvent e)
2959 public void enterPdbId_actionPerformed(ActionEvent e)
2964 public void pdbFile_actionPerformed(ActionEvent e)
2969 public void invertColSel_actionPerformed(ActionEvent e)
2974 public void tabSelectionChanged(int sel)
2979 public void tabbedPane_mousePressed(MouseEvent e)
2984 public void tabbedPane_focusGained(FocusEvent e)
2989 public void save_actionPerformed(ActionEvent e)
2994 public void reload_actionPerformed(ActionEvent e)
2999 public void newView_actionPerformed(ActionEvent e)
3004 public void textColour_actionPerformed(ActionEvent e)
3009 public void idRightAlign_actionPerformed(ActionEvent e)
3014 public void expandViews_actionPerformed(ActionEvent e)
3019 public void gatherViews_actionPerformed(ActionEvent e)
3024 public void buildTreeMenu()
3029 public void pageSetup_actionPerformed(ActionEvent e)
3034 public void alignmentProperties()
3039 protected void expand_newalign(ActionEvent e)
3041 // TODO Auto-generated method stub
3045 protected boolean isShowAutoCalculatedAbove()
3047 return showAutoCalculatedAbove;
3050 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3052 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3055 protected SequenceAnnotationOrder getAnnotationSortOrder()
3057 return annotationSortOrder;
3060 protected void setAnnotationSortOrder(
3061 SequenceAnnotationOrder annotationSortOrder)
3063 this.annotationSortOrder = annotationSortOrder;
3066 public Map<KeyStroke, JMenuItem> getAccelerators()
3068 return this.accelerators;
3072 * Returns the selected index of the tabbed pane, or -1 if none selected
3073 * (including the case where the tabbed pane has not been made visible).
3077 public int getTabIndex()
3079 return tabbedPane.getSelectedIndex();
3082 public JPanel getStatusPanel()
3088 * Sets a reference to the containing split frame. Also makes the 'toggle
3089 * split view' menu item visible and checked.
3093 public void setSplitFrame(SplitContainerI sf)
3095 this.splitFrame = sf;
3098 this.showComplementMenuItem.setVisible(true);
3099 this.showComplementMenuItem.setState(true);
3103 public SplitContainerI getSplitViewContainer()
3105 return this.splitFrame;
3108 protected void showComplement_actionPerformed(boolean state)