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 final boolean autoFirst = Cache.getDefault(
1299 Preferences.SHOW_AUTOCALC_ABOVE, false);
1300 showAutoFirst.setSelected(autoFirst);
1301 setShowAutoCalculatedAbove(autoFirst);
1302 showAutoFirst.addActionListener(new ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1308 sortAnnotations_actionPerformed();
1311 showAutoLast.setSelected(!showAutoFirst.isSelected());
1312 showAutoLast.addActionListener(new ActionListener()
1315 public void actionPerformed(ActionEvent e)
1317 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1318 sortAnnotations_actionPerformed();
1322 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1323 nucleotideColour.addActionListener(new ActionListener()
1326 public void actionPerformed(ActionEvent e)
1328 nucleotideColour_actionPerformed(e);
1332 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1333 tcoffeeColour.setEnabled(false);
1334 tcoffeeColour.addActionListener(new ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 tcoffeeColorScheme_actionPerformed(e);
1344 JMenuItem deleteGroups = new JMenuItem(
1345 MessageManager.getString("action.undefine_groups"));
1346 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1347 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1348 al = new ActionListener()
1351 public void actionPerformed(ActionEvent e)
1353 deleteGroups_actionPerformed(e);
1356 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1358 JMenuItem createGroup = new JMenuItem(
1359 MessageManager.getString("action.create_groups"));
1360 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1361 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1362 al = new ActionListener()
1365 public void actionPerformed(ActionEvent e)
1367 createGroup_actionPerformed(e);
1370 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1372 JMenuItem unGroup = new JMenuItem(
1373 MessageManager.getString("action.remove_group"));
1374 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1375 .getDefaultToolkit().getMenuShortcutKeyMask()
1376 | KeyEvent.SHIFT_MASK, false);
1377 al = new ActionListener()
1380 public void actionPerformed(ActionEvent e)
1382 unGroup_actionPerformed(e);
1385 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1387 copy.setText(MessageManager.getString("action.copy"));
1388 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1389 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1391 al = new ActionListener()
1394 public void actionPerformed(ActionEvent e)
1396 copy_actionPerformed(e);
1399 addMenuActionAndAccelerator(keyStroke, copy, al);
1401 cut.setText(MessageManager.getString("action.cut"));
1402 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1403 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1404 al = new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 cut_actionPerformed(e);
1412 addMenuActionAndAccelerator(keyStroke, cut, al);
1414 JMenuItem delete = new JMenuItem(
1415 MessageManager.getString("action.delete"));
1416 delete.addActionListener(new ActionListener()
1419 public void actionPerformed(ActionEvent e)
1421 delete_actionPerformed(e);
1425 pasteMenu.setText(MessageManager.getString("action.paste"));
1426 JMenuItem pasteNew = new JMenuItem(
1427 MessageManager.getString("label.to_new_alignment"));
1428 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1429 .getDefaultToolkit().getMenuShortcutKeyMask()
1430 | KeyEvent.SHIFT_MASK, false);
1431 al = new ActionListener()
1434 public void actionPerformed(ActionEvent e)
1436 pasteNew_actionPerformed(e);
1439 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1441 JMenuItem pasteThis = new JMenuItem(
1442 MessageManager.getString("label.to_this_alignment"));
1443 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1444 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1445 al = new ActionListener()
1448 public void actionPerformed(ActionEvent e)
1450 pasteThis_actionPerformed(e);
1453 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1455 applyToAllGroups.setText(MessageManager
1456 .getString("label.apply_colour_to_all_groups"));
1457 applyToAllGroups.addActionListener(new ActionListener()
1460 public void actionPerformed(ActionEvent e)
1462 applyToAllGroups_actionPerformed(e);
1465 JMenuItem createPNG = new JMenuItem("PNG");
1466 createPNG.addActionListener(new ActionListener()
1469 public void actionPerformed(ActionEvent e)
1474 createPNG.setActionCommand(MessageManager
1475 .getString("label.save_png_image"));
1477 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1478 font.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 font_actionPerformed(e);
1486 seqLimits.setText(MessageManager
1487 .getString("label.show_sequence_limits"));
1488 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1489 seqLimits.addActionListener(new ActionListener()
1492 public void actionPerformed(ActionEvent e)
1494 seqLimit_actionPerformed(e);
1497 JMenuItem epsFile = new JMenuItem("EPS");
1498 epsFile.addActionListener(new ActionListener()
1501 public void actionPerformed(ActionEvent e)
1507 JMenuItem createSVG = new JMenuItem("SVG");
1508 createSVG.addActionListener(new ActionListener()
1511 public void actionPerformed(ActionEvent e)
1517 JMenuItem loadTreeMenuItem = new JMenuItem(
1518 MessageManager.getString("label.load_associated_tree"));
1519 loadTreeMenuItem.setActionCommand(MessageManager
1520 .getString("label.load_tree_for_sequence_set"));
1521 loadTreeMenuItem.addActionListener(new ActionListener()
1524 public void actionPerformed(ActionEvent e)
1526 loadTreeMenuItem_actionPerformed(e);
1530 scaleAbove.setVisible(false);
1531 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1532 scaleAbove.addActionListener(new ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 scaleAbove_actionPerformed(e);
1540 scaleLeft.setVisible(false);
1541 scaleLeft.setSelected(true);
1542 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1543 scaleLeft.addActionListener(new ActionListener()
1546 public void actionPerformed(ActionEvent e)
1548 scaleLeft_actionPerformed(e);
1551 scaleRight.setVisible(false);
1552 scaleRight.setSelected(true);
1553 scaleRight.setText(MessageManager.getString("action.scale_right"));
1554 scaleRight.addActionListener(new ActionListener()
1557 public void actionPerformed(ActionEvent e)
1559 scaleRight_actionPerformed(e);
1562 centreColumnLabelsMenuItem.setVisible(true);
1563 centreColumnLabelsMenuItem.setState(false);
1564 centreColumnLabelsMenuItem.setText(MessageManager
1565 .getString("label.centre_column_labels"));
1566 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1569 public void actionPerformed(ActionEvent e)
1571 centreColumnLabels_actionPerformed(e);
1574 followHighlightMenuItem.setVisible(true);
1575 followHighlightMenuItem.setState(true);
1576 followHighlightMenuItem.setText(MessageManager
1577 .getString("label.automatic_scrolling"));
1578 followHighlightMenuItem.addActionListener(new ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 followHighlight_actionPerformed();
1589 JMenuItem modifyPID = new JMenuItem(
1590 MessageManager.getString("label.modify_identity_thereshold"));
1591 modifyPID.addActionListener(new ActionListener()
1594 public void actionPerformed(ActionEvent e)
1596 modifyPID_actionPerformed(e);
1599 modifyConservation.setText(MessageManager
1600 .getString("label.modify_conservation_thereshold"));
1601 modifyConservation.addActionListener(new ActionListener()
1604 public void actionPerformed(ActionEvent e)
1606 modifyConservation_actionPerformed(e);
1610 .setText(MessageManager.getString("action.by_tree_order"));
1611 sort.setText(MessageManager.getString("action.sort"));
1612 sort.addMenuListener(new MenuListener()
1615 public void menuSelected(MenuEvent e)
1621 public void menuDeselected(MenuEvent e)
1626 public void menuCanceled(MenuEvent e)
1630 sortByAnnotScore.setText(MessageManager
1631 .getString("label.sort_by_score"));
1632 sort.add(sortByAnnotScore);
1633 sort.addMenuListener(new javax.swing.event.MenuListener()
1637 public void menuCanceled(MenuEvent e)
1642 public void menuDeselected(MenuEvent e)
1647 public void menuSelected(MenuEvent e)
1649 buildSortByAnnotationScoresMenu();
1652 sortByAnnotScore.setVisible(false);
1655 .setText(MessageManager.getString("action.calculate_tree"));
1657 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1658 padGapsMenuitem.setState(jalview.bin.Cache
1659 .getDefault("PAD_GAPS", false));
1660 padGapsMenuitem.addActionListener(new ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 padGapsMenuitem_actionPerformed(e);
1668 JMenuItem vamsasStore = new JMenuItem(
1669 MessageManager.getString("label.vamsas_store"));
1670 vamsasStore.setVisible(false);
1671 vamsasStore.addActionListener(new ActionListener()
1674 public void actionPerformed(ActionEvent e)
1676 vamsasStore_actionPerformed(e);
1679 showTranslation.setText(MessageManager
1680 .getString("label.translate_cDNA"));
1681 showTranslation.addActionListener(new ActionListener()
1684 public void actionPerformed(ActionEvent e)
1686 showTranslation_actionPerformed(e);
1690 JMenuItem extractScores = new JMenuItem(
1691 MessageManager.getString("label.extract_scores"));
1692 extractScores.addActionListener(new ActionListener()
1695 public void actionPerformed(ActionEvent e)
1697 extractScores_actionPerformed(e);
1700 extractScores.setVisible(true);
1701 // JBPNote: TODO: make gui for regex based score extraction
1703 // for show products actions see AlignFrame.canShowProducts
1704 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1706 JMenuItem openFeatureSettings = new JMenuItem(
1707 MessageManager.getString("action.feature_settings"));
1708 openFeatureSettings.addActionListener(new ActionListener()
1711 public void actionPerformed(ActionEvent e)
1713 featureSettings_actionPerformed(e);
1716 JMenuItem fetchSequence = new JMenuItem(
1717 MessageManager.getString("label.fetch_sequences"));
1718 fetchSequence.addActionListener(new ActionListener()
1721 public void actionPerformed(ActionEvent e)
1723 fetchSequence_actionPerformed(e);
1727 JMenuItem annotationColour = new JMenuItem(
1728 MessageManager.getString("action.by_annotation"));
1729 annotationColour.addActionListener(new ActionListener()
1732 public void actionPerformed(ActionEvent e)
1734 annotationColour_actionPerformed(e);
1738 JMenuItem annotationColumn = new JMenuItem(
1739 MessageManager.getString("action.select_by_annotation"));
1740 annotationColumn.addActionListener(new ActionListener()
1743 public void actionPerformed(ActionEvent e)
1745 annotationColumn_actionPerformed(e);
1749 rnahelicesColour.setText(MessageManager
1750 .getString("action.by_rna_helixes"));
1751 rnahelicesColour.addActionListener(new ActionListener()
1754 public void actionPerformed(ActionEvent e)
1756 rnahelicesColour_actionPerformed(e);
1760 JMenuItem associatedData = new JMenuItem(
1761 MessageManager.getString("label.load_features_annotations"));
1762 associatedData.addActionListener(new ActionListener()
1765 public void actionPerformed(ActionEvent e)
1767 associatedData_actionPerformed(e);
1770 autoCalculate.setText(MessageManager
1771 .getString("label.autocalculate_consensus"));
1772 autoCalculate.setState(jalview.bin.Cache.getDefault(
1773 "AUTO_CALC_CONSENSUS", true));
1774 autoCalculate.addActionListener(new ActionListener()
1777 public void actionPerformed(ActionEvent e)
1779 autoCalculate_actionPerformed(e);
1782 sortByTree.setText(MessageManager
1783 .getString("label.sort_alignment_new_tree"));
1785 .setToolTipText("<html>"
1787 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1789 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1790 sortByTree.addActionListener(new ActionListener()
1793 public void actionPerformed(ActionEvent e)
1795 sortByTreeOption_actionPerformed(e);
1799 listenToViewSelections.setText(MessageManager
1800 .getString("label.listen_for_selections"));
1801 listenToViewSelections
1802 .setToolTipText("<html>"
1804 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1805 listenToViewSelections.setState(false);
1806 listenToViewSelections.addActionListener(new ActionListener()
1809 public void actionPerformed(ActionEvent e)
1811 listenToViewSelections_actionPerformed(e);
1815 JMenu addSequenceMenu = new JMenu(
1816 MessageManager.getString("label.add_sequences"));
1817 JMenuItem addFromFile = new JMenuItem(
1818 MessageManager.getString("label.from_file"));
1819 addFromFile.addActionListener(new ActionListener()
1822 public void actionPerformed(ActionEvent e)
1824 addFromFile_actionPerformed(e);
1827 JMenuItem addFromText = new JMenuItem(
1828 MessageManager.getString("label.from_textbox"));
1829 addFromText.addActionListener(new ActionListener()
1832 public void actionPerformed(ActionEvent e)
1834 addFromText_actionPerformed(e);
1837 JMenuItem addFromURL = new JMenuItem(
1838 MessageManager.getString("label.from_url"));
1839 addFromURL.addActionListener(new ActionListener()
1842 public void actionPerformed(ActionEvent e)
1844 addFromURL_actionPerformed(e);
1847 JMenuItem exportFeatures = new JMenuItem(
1848 MessageManager.getString("label.export_features"));
1849 exportFeatures.addActionListener(new ActionListener()
1852 public void actionPerformed(ActionEvent e)
1854 exportFeatures_actionPerformed(e);
1857 JMenuItem exportAnnotations = new JMenuItem(
1858 MessageManager.getString("label.export_annotations"));
1859 exportAnnotations.addActionListener(new ActionListener()
1862 public void actionPerformed(ActionEvent e)
1864 exportAnnotations_actionPerformed(e);
1867 statusPanel.setLayout(new GridLayout());
1868 JMenuItem showAllSeqs = new JMenuItem(
1869 MessageManager.getString("label.all_sequences"));
1870 showAllSeqs.setToolTipText(MessageManager
1871 .getString("label.toggle_sequence_visibility"));
1872 showAllSeqs.addActionListener(new ActionListener()
1875 public void actionPerformed(ActionEvent e)
1877 showAllSeqs_actionPerformed(e);
1880 JMenuItem showAllColumns = new JMenuItem(
1881 MessageManager.getString("label.all_columns"));
1882 showAllColumns.setToolTipText(MessageManager
1883 .getString("label.toggle_columns_visibility"));
1884 showAllColumns.addActionListener(new ActionListener()
1887 public void actionPerformed(ActionEvent e)
1889 showAllColumns_actionPerformed(e);
1892 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1893 JMenuItem hideSelSequences = new JMenuItem(
1894 MessageManager.getString("label.selected_sequences"));
1895 hideSelSequences.setToolTipText(MessageManager
1896 .getString("label.toggle_sequence_visibility"));
1897 hideSelSequences.addActionListener(new ActionListener()
1900 public void actionPerformed(ActionEvent e)
1902 hideSelSequences_actionPerformed(e);
1905 JMenuItem hideSelColumns = new JMenuItem(
1906 MessageManager.getString("label.selected_columns"));
1907 hideSelColumns.setToolTipText(MessageManager
1908 .getString("label.toggle_columns_visibility"));
1909 hideSelColumns.addActionListener(new ActionListener()
1912 public void actionPerformed(ActionEvent e)
1914 hideSelColumns_actionPerformed(e);
1917 JMenuItem hideAllSelection = new JMenuItem(
1918 MessageManager.getString("label.selected_region"));
1919 hideAllSelection.addActionListener(new ActionListener()
1922 public void actionPerformed(ActionEvent e)
1924 hideAllSelection_actionPerformed(e);
1927 // TODO: should be hidden if no selection exists.
1928 JMenuItem hideAllButSelection = new JMenuItem(
1929 MessageManager.getString("label.all_but_selected_region"));
1930 hideAllButSelection.addActionListener(new ActionListener()
1933 public void actionPerformed(ActionEvent e)
1935 hideAllButSelection_actionPerformed(e);
1938 JMenuItem showAllhidden = new JMenuItem(
1939 MessageManager.getString("label.all_sequences_columns"));
1940 showAllhidden.setToolTipText(MessageManager
1941 .getString("label.toggles_visibility_hidden_selected_regions"));
1942 showAllhidden.addActionListener(new ActionListener()
1945 public void actionPerformed(ActionEvent e)
1947 showAllhidden_actionPerformed(e);
1950 hiddenMarkers.setText(MessageManager
1951 .getString("action.show_hidden_markers"));
1952 hiddenMarkers.addActionListener(new ActionListener()
1955 public void actionPerformed(ActionEvent e)
1957 hiddenMarkers_actionPerformed(e);
1961 JMenuItem invertColSel = new JMenuItem(
1962 MessageManager.getString("action.invert_column_selection"));
1963 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
1964 .getDefaultToolkit().getMenuShortcutKeyMask()
1965 | KeyEvent.ALT_MASK, false);
1966 al = new ActionListener()
1969 public void actionPerformed(ActionEvent e)
1971 invertColSel_actionPerformed(e);
1974 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1976 showComplementMenuItem.setVisible(false);
1977 showComplementMenuItem.addActionListener(new ActionListener()
1980 public void actionPerformed(ActionEvent e)
1982 showComplement_actionPerformed(showComplementMenuItem.getState());
1986 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1989 public void stateChanged(ChangeEvent evt)
1991 JTabbedPane pane = (JTabbedPane) evt.getSource();
1992 int sel = pane.getSelectedIndex();
1993 tabSelectionChanged(sel);
1996 tabbedPane.addMouseListener(new MouseAdapter()
1999 public void mousePressed(MouseEvent e)
2001 tabbedPane_mousePressed(e);
2004 tabbedPane.addFocusListener(new FocusAdapter()
2007 public void focusGained(FocusEvent e)
2009 tabbedPane_focusGained(e);
2013 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
2014 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
2015 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2016 al = new ActionListener()
2019 public void actionPerformed(ActionEvent e)
2021 save_actionPerformed(e);
2024 addMenuActionAndAccelerator(keyStroke, save, al);
2026 reload.setEnabled(false);
2027 reload.setText(MessageManager.getString("action.reload"));
2028 reload.addActionListener(new ActionListener()
2031 public void actionPerformed(ActionEvent e)
2033 reload_actionPerformed(e);
2037 JMenuItem newView = new JMenuItem(
2038 MessageManager.getString("action.new_view"));
2039 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
2040 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2041 al = new ActionListener()
2044 public void actionPerformed(ActionEvent e)
2046 newView_actionPerformed(e);
2049 addMenuActionAndAccelerator(keyStroke, newView, al);
2051 tabbedPane.setToolTipText("<html><i>"
2052 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2054 JMenuItem textColour = new JMenuItem(
2055 MessageManager.getString("action.set_text_colour"));
2056 textColour.addActionListener(new ActionListener()
2059 public void actionPerformed(ActionEvent e)
2061 textColour_actionPerformed(e);
2064 formatMenu.setText(MessageManager.getString("action.format"));
2065 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
2066 idRightAlign.setText(MessageManager
2067 .getString("label.right_align_sequence_id"));
2068 idRightAlign.addActionListener(new ActionListener()
2071 public void actionPerformed(ActionEvent e)
2073 idRightAlign_actionPerformed(e);
2077 gatherViews.setEnabled(false);
2078 gatherViews.setText(MessageManager.getString("action.gather_views"));
2079 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
2080 al = new ActionListener()
2083 public void actionPerformed(ActionEvent e)
2085 gatherViews_actionPerformed(e);
2088 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
2090 expandViews.setEnabled(false);
2091 expandViews.setText(MessageManager.getString("action.expand_views"));
2092 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
2093 al = new ActionListener()
2096 public void actionPerformed(ActionEvent e)
2098 expandViews_actionPerformed(e);
2101 addMenuActionAndAccelerator(keyStroke, expandViews, al);
2103 JMenuItem pageSetup = new JMenuItem(
2104 MessageManager.getString("action.page_setup"));
2105 pageSetup.addActionListener(new ActionListener()
2108 public void actionPerformed(ActionEvent e)
2110 pageSetup_actionPerformed(e);
2113 JMenuItem alignmentProperties = new JMenuItem(
2114 MessageManager.getString("label.alignment_props"));
2115 alignmentProperties.addActionListener(new ActionListener()
2118 public void actionPerformed(ActionEvent actionEvent)
2120 alignmentProperties();
2123 JMenu tooltipSettingsMenu = new JMenu(
2124 MessageManager.getString("label.sequence_id_tooltip"));
2125 JMenu autoAnnMenu = new JMenu(
2126 MessageManager.getString("label.autocalculated_annotation"));
2128 JMenu exportImageMenu = new JMenu(
2129 MessageManager.getString("label.export_image"));
2130 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
2131 alignFrameMenuBar.add(fileMenu);
2132 alignFrameMenuBar.add(editMenu);
2133 alignFrameMenuBar.add(selectMenu);
2134 alignFrameMenuBar.add(viewMenu);
2135 alignFrameMenuBar.add(annotationsMenu);
2136 alignFrameMenuBar.add(formatMenu);
2137 alignFrameMenuBar.add(colourMenu);
2138 alignFrameMenuBar.add(calculateMenu);
2139 alignFrameMenuBar.add(webService);
2140 fileMenu.add(fetchSequence);
2141 fileMenu.add(addSequenceMenu);
2142 fileMenu.add(reload);
2143 fileMenu.addSeparator();
2144 fileMenu.add(vamsasStore);
2146 fileMenu.add(saveAs);
2147 fileMenu.add(outputTextboxMenu);
2148 fileMenu.add(pageSetup);
2149 fileMenu.add(printMenuItem);
2150 fileMenu.addSeparator();
2151 fileMenu.add(exportImageMenu);
2152 fileMenu.add(exportFeatures);
2153 fileMenu.add(exportAnnotations);
2154 fileMenu.add(loadTreeMenuItem);
2155 fileMenu.add(associatedData);
2156 fileMenu.addSeparator();
2157 fileMenu.add(closeMenuItem);
2158 editMenu.add(undoMenuItem);
2159 editMenu.add(redoMenuItem);
2162 editMenu.add(pasteMenu);
2163 editMenu.add(delete);
2164 editMenu.addSeparator();
2165 editMenu.add(remove2LeftMenuItem);
2166 editMenu.add(remove2RightMenuItem);
2167 editMenu.add(removeGappedColumnMenuItem);
2168 editMenu.add(removeAllGapsMenuItem);
2169 editMenu.add(removeRedundancyMenuItem);
2170 editMenu.addSeparator();
2171 // dont add these yet in the CVS build - they cannot be undone!
2172 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2173 // editMenu.add(justifyLeftMenuItem);
2174 // editMenu.add(justifyRightMenuItem);
2175 // editMenu.addSeparator();
2176 editMenu.add(padGapsMenuitem);
2178 viewMenu.add(newView);
2179 viewMenu.add(expandViews);
2180 viewMenu.add(gatherViews);
2181 viewMenu.addSeparator();
2182 viewMenu.add(showMenu);
2183 viewMenu.add(hideMenu);
2184 viewMenu.add(showComplementMenuItem);
2185 viewMenu.addSeparator();
2186 viewMenu.add(followHighlightMenuItem);
2187 viewMenu.addSeparator();
2188 viewMenu.add(showSeqFeatures);
2189 // viewMenu.add(showSeqFeaturesHeight);
2190 viewMenu.add(openFeatureSettings);
2191 tooltipSettingsMenu.add(showDbRefsMenuitem);
2192 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2193 viewMenu.add(tooltipSettingsMenu);
2194 viewMenu.addSeparator();
2195 viewMenu.add(alignmentProperties);
2196 viewMenu.addSeparator();
2197 viewMenu.add(overviewMenuItem);
2199 annotationsMenu.add(annotationPanelMenuItem);
2200 annotationsMenu.addSeparator();
2201 annotationsMenu.add(showAllAlAnnotations);
2202 annotationsMenu.add(hideAllAlAnnotations);
2203 annotationsMenu.addSeparator();
2204 annotationsMenu.add(showAllSeqAnnotations);
2205 annotationsMenu.add(hideAllSeqAnnotations);
2206 annotationsMenu.add(sortAnnBySequence);
2207 annotationsMenu.add(sortAnnByLabel);
2208 annotationsMenu.addSeparator();
2209 autoAnnMenu.add(showAutoFirst);
2210 autoAnnMenu.add(showAutoLast);
2211 autoAnnMenu.addSeparator();
2212 autoAnnMenu.add(applyAutoAnnotationSettings);
2213 autoAnnMenu.add(showConsensusHistogram);
2214 autoAnnMenu.add(showSequenceLogo);
2215 autoAnnMenu.add(normaliseSequenceLogo);
2216 autoAnnMenu.addSeparator();
2217 autoAnnMenu.add(showGroupConservation);
2218 autoAnnMenu.add(showGroupConsensus);
2219 annotationsMenu.add(autoAnnMenu);
2221 colourMenu.add(applyToAllGroups);
2222 colourMenu.add(textColour);
2223 colourMenu.addSeparator();
2224 colourMenu.add(noColourmenuItem);
2225 colourMenu.add(clustalColour);
2226 colourMenu.add(BLOSUM62Colour);
2227 colourMenu.add(PIDColour);
2228 colourMenu.add(zappoColour);
2229 colourMenu.add(taylorColour);
2230 colourMenu.add(hydrophobicityColour);
2231 colourMenu.add(helixColour);
2232 colourMenu.add(strandColour);
2233 colourMenu.add(turnColour);
2234 colourMenu.add(buriedColour);
2235 colourMenu.add(nucleotideColour);
2236 colourMenu.add(purinePyrimidineColour);
2237 colourMenu.add(RNAInteractionColour);
2238 // colourMenu.add(covariationColour);
2239 colourMenu.add(tcoffeeColour);
2240 colourMenu.add(userDefinedColour);
2241 colourMenu.addSeparator();
2242 colourMenu.add(conservationMenuItem);
2243 colourMenu.add(modifyConservation);
2244 colourMenu.add(abovePIDThreshold);
2245 colourMenu.add(modifyPID);
2246 colourMenu.add(annotationColour);
2247 colourMenu.add(rnahelicesColour);
2248 calculateMenu.add(sort);
2249 calculateMenu.add(calculateTree);
2250 calculateMenu.addSeparator();
2251 calculateMenu.add(pairwiseAlignmentMenuItem);
2252 calculateMenu.add(PCAMenuItem);
2253 calculateMenu.addSeparator();
2254 calculateMenu.add(showTranslation);
2255 calculateMenu.add(showProducts);
2256 calculateMenu.add(autoCalculate);
2257 calculateMenu.add(sortByTree);
2258 calculateMenu.addSeparator();
2259 calculateMenu.add(extractScores);
2260 webServiceNoServices = new JMenuItem(
2261 MessageManager.getString("label.no_services"));
2262 webService.add(webServiceNoServices);
2263 pasteMenu.add(pasteNew);
2264 pasteMenu.add(pasteThis);
2265 sort.add(sortIDMenuItem);
2266 sort.add(sortLengthMenuItem);
2267 sort.add(sortGroupMenuItem);
2268 sort.add(sortPairwiseMenuItem);
2269 sort.add(sortByTreeMenu);
2270 exportImageMenu.add(htmlMenuItem);
2271 exportImageMenu.add(epsFile);
2272 exportImageMenu.add(createPNG);
2273 exportImageMenu.add(createBioJS);
2274 exportImageMenu.add(createSVG);
2275 addSequenceMenu.add(addFromFile);
2276 addSequenceMenu.add(addFromText);
2277 addSequenceMenu.add(addFromURL);
2278 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2279 statusPanel.add(statusBar, null);
2280 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2281 showMenu.add(showAllColumns);
2282 showMenu.add(showAllSeqs);
2283 showMenu.add(showAllhidden);
2284 hideMenu.add(hideSelColumns);
2285 hideMenu.add(hideSelSequences);
2286 hideMenu.add(hideAllSelection);
2287 hideMenu.add(hideAllButSelection);
2289 formatMenu.add(font);
2290 formatMenu.addSeparator();
2291 formatMenu.add(wrapMenuItem);
2292 formatMenu.add(scaleAbove);
2293 formatMenu.add(scaleLeft);
2294 formatMenu.add(scaleRight);
2295 formatMenu.add(seqLimits);
2296 formatMenu.add(idRightAlign);
2297 formatMenu.add(hiddenMarkers);
2298 formatMenu.add(viewBoxesMenuItem);
2299 formatMenu.add(viewTextMenuItem);
2300 formatMenu.add(colourTextMenuItem);
2301 formatMenu.add(renderGapsMenuItem);
2302 formatMenu.add(centreColumnLabelsMenuItem);
2303 formatMenu.add(showNonconservedMenuItem);
2304 selectMenu.add(findMenuItem);
2305 selectMenu.addSeparator();
2306 selectMenu.add(selectAllSequenceMenuItem);
2307 selectMenu.add(deselectAllSequenceMenuItem);
2308 selectMenu.add(invertSequenceMenuItem);
2309 selectMenu.add(invertColSel);
2310 selectMenu.add(createGroup);
2311 selectMenu.add(unGroup);
2312 selectMenu.add(grpsFromSelection);
2313 selectMenu.add(deleteGroups);
2314 selectMenu.add(annotationColumn);
2315 calculateMenu.add(expandAlignment);
2316 // TODO - determine if the listenToViewSelections button is needed : see bug
2318 // selectMenu.addSeparator();
2319 // selectMenu.add(listenToViewSelections);
2323 * Adds the given action listener and key accelerator to the given menu item.
2324 * Also saves in a lookup table to support lookup of action by key stroke.
2328 * @param actionListener
2330 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2331 JMenuItem menuItem, ActionListener actionListener)
2333 menuItem.setAccelerator(keyStroke);
2334 accelerators.put(keyStroke, menuItem);
2335 menuItem.addActionListener(actionListener);
2339 * Action on clicking sort annotations by type.
2343 protected void sortAnnotations_actionPerformed()
2348 * Action on clicking Show all annotations.
2350 * @param forSequences
2351 * update sequence-related annotations
2352 * @param forAlignment
2353 * update non-sequence-related annotations
2355 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2356 boolean forAlignment)
2358 setAnnotationsVisibility(true, forSequences, forAlignment);
2362 * Action on clicking Hide all annotations.
2364 * @param forSequences
2365 * update sequence-related annotations
2366 * @param forAlignment
2367 * update non-sequence-related annotations
2369 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2370 boolean forAlignment)
2372 setAnnotationsVisibility(false, forSequences, forAlignment);
2376 * Set the visibility of annotations to true or false. Can act on
2377 * sequence-related annotations, or alignment-related, or both.
2380 * @param forSequences
2381 * update sequence-related annotations
2382 * @param forAlignment
2383 * update non-sequence-related annotations
2385 protected void setAnnotationsVisibility(boolean visible,
2386 boolean forSequences, boolean forAlignment)
2391 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2393 // TODO Auto-generated method stub
2397 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2399 // TODO Auto-generated method stub
2403 protected void showAllhidden_actionPerformed(ActionEvent e)
2405 // TODO Auto-generated method stub
2409 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2411 // TODO Auto-generated method stub
2415 protected void hideAllSelection_actionPerformed(ActionEvent e)
2417 // TODO Auto-generated method stub
2421 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2423 // TODO Auto-generated method stub
2427 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2429 // TODO Auto-generated method stub
2433 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2435 // TODO Auto-generated method stub
2439 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2441 // TODO Auto-generated method stub
2445 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2447 // TODO Auto-generated method stub
2451 protected void showGroupConservation_actionPerformed(ActionEvent e)
2453 // TODO Auto-generated method stub
2457 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2459 // TODO Auto-generated method stub
2463 protected void showSeqFeaturesHeight_actionPerformed(
2464 ActionEvent actionEvent)
2466 // TODO Auto-generated method stub
2470 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2472 // TODO Auto-generated method stub
2476 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2478 // TODO Auto-generated method stub
2482 protected void followHighlight_actionPerformed()
2484 // TODO Auto-generated method stub
2488 protected void showNpFeats_actionPerformed(ActionEvent e)
2490 // TODO Auto-generated method stub
2494 protected void showDbRefs_actionPerformed(ActionEvent e)
2496 // TODO Auto-generated method stub
2500 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2504 protected void buildSortByAnnotationScoresMenu()
2508 protected void extractScores_actionPerformed(ActionEvent e)
2512 protected void outputText_actionPerformed(ActionEvent e)
2516 public void addFromFile_actionPerformed(ActionEvent e)
2521 public void addFromText_actionPerformed(ActionEvent e)
2526 public void addFromURL_actionPerformed(ActionEvent e)
2531 public void exportFeatures_actionPerformed(ActionEvent e)
2536 public void exportAnnotations_actionPerformed(ActionEvent e)
2541 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2545 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2550 protected void closeMenuItem_actionPerformed(boolean b)
2554 protected void redoMenuItem_actionPerformed(ActionEvent e)
2558 protected void undoMenuItem_actionPerformed(ActionEvent e)
2562 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2566 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2570 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2574 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2578 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2582 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2586 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2590 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2594 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2598 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2602 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2606 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2610 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2614 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2618 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2622 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2626 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2630 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2634 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2638 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2642 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2646 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2650 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2654 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2658 protected void clustalColour_actionPerformed(ActionEvent e)
2662 protected void zappoColour_actionPerformed(ActionEvent e)
2666 protected void taylorColour_actionPerformed(ActionEvent e)
2670 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2674 protected void helixColour_actionPerformed(ActionEvent e)
2678 protected void strandColour_actionPerformed(ActionEvent e)
2682 protected void turnColour_actionPerformed(ActionEvent e)
2686 protected void buriedColour_actionPerformed(ActionEvent e)
2690 protected void userDefinedColour_actionPerformed(ActionEvent e)
2694 protected void PIDColour_actionPerformed(ActionEvent e)
2698 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2702 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2706 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2711 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2714 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2718 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2722 protected void printMenuItem_actionPerformed(ActionEvent e)
2726 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2730 protected void findMenuItem_actionPerformed(ActionEvent e)
2734 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2738 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2742 protected void nucleotideColour_actionPerformed(ActionEvent e)
2746 protected void deleteGroups_actionPerformed(ActionEvent e)
2750 protected void createGroup_actionPerformed(ActionEvent e)
2754 protected void unGroup_actionPerformed(ActionEvent e)
2758 protected void copy_actionPerformed(ActionEvent e)
2762 protected void cut_actionPerformed(ActionEvent e)
2766 protected void delete_actionPerformed(ActionEvent e)
2770 protected void pasteNew_actionPerformed(ActionEvent e)
2774 protected void pasteThis_actionPerformed(ActionEvent e)
2778 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2782 public void createPNG(java.io.File f)
2786 protected void font_actionPerformed(ActionEvent e)
2790 protected void seqLimit_actionPerformed(ActionEvent e)
2794 public void seqDBRef_actionPerformed(ActionEvent e)
2799 public void createEPS(java.io.File f)
2803 public void createSVG(java.io.File f)
2808 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2814 * Template method to handle the 'load T-Coffee scores' menu event.
2816 * Subclasses override this method to provide a custom action.
2821 protected void loadScores_actionPerformed(ActionEvent event)
2827 * Template method to handle the 'Color T-Coffee scores' menu event.
2829 * Subclasses override this method to provide a custom action.
2834 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2839 protected void jpred_actionPerformed(ActionEvent e)
2843 protected void scaleAbove_actionPerformed(ActionEvent e)
2847 protected void scaleLeft_actionPerformed(ActionEvent e)
2851 protected void scaleRight_actionPerformed(ActionEvent e)
2855 protected void modifyPID_actionPerformed(ActionEvent e)
2859 protected void modifyConservation_actionPerformed(ActionEvent e)
2863 protected void saveAs_actionPerformed(ActionEvent e)
2867 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2871 public void vamsasStore_actionPerformed(ActionEvent e)
2876 public void vamsasLoad_actionPerformed(ActionEvent e)
2881 public void showTranslation_actionPerformed(ActionEvent e)
2886 public void featureSettings_actionPerformed(ActionEvent e)
2891 public void fetchSequence_actionPerformed(ActionEvent e)
2896 public void smoothFont_actionPerformed(ActionEvent e)
2901 public void annotationColour_actionPerformed(ActionEvent e)
2906 public void annotationColumn_actionPerformed(ActionEvent e)
2911 public void rnahelicesColour_actionPerformed(ActionEvent e)
2916 public void associatedData_actionPerformed(ActionEvent e)
2921 public void autoCalculate_actionPerformed(ActionEvent e)
2926 public void sortByTreeOption_actionPerformed(ActionEvent e)
2931 public void showAllSeqs_actionPerformed(ActionEvent e)
2936 public void showAllColumns_actionPerformed(ActionEvent e)
2941 public void hideSelSequences_actionPerformed(ActionEvent e)
2946 public void hideSelColumns_actionPerformed(ActionEvent e)
2951 public void hiddenMarkers_actionPerformed(ActionEvent e)
2956 public void findPdbId_actionPerformed(ActionEvent e)
2961 public void enterPdbId_actionPerformed(ActionEvent e)
2966 public void pdbFile_actionPerformed(ActionEvent e)
2971 public void invertColSel_actionPerformed(ActionEvent e)
2976 public void tabSelectionChanged(int sel)
2981 public void tabbedPane_mousePressed(MouseEvent e)
2986 public void tabbedPane_focusGained(FocusEvent e)
2991 public void save_actionPerformed(ActionEvent e)
2996 public void reload_actionPerformed(ActionEvent e)
3001 public void newView_actionPerformed(ActionEvent e)
3006 public void textColour_actionPerformed(ActionEvent e)
3011 public void idRightAlign_actionPerformed(ActionEvent e)
3016 public void expandViews_actionPerformed(ActionEvent e)
3021 public void gatherViews_actionPerformed(ActionEvent e)
3026 public void buildTreeMenu()
3031 public void pageSetup_actionPerformed(ActionEvent e)
3036 public void alignmentProperties()
3041 protected void expand_newalign(ActionEvent e)
3043 // TODO Auto-generated method stub
3047 protected boolean isShowAutoCalculatedAbove()
3049 return showAutoCalculatedAbove;
3052 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3054 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3057 protected SequenceAnnotationOrder getAnnotationSortOrder()
3059 return annotationSortOrder;
3062 protected void setAnnotationSortOrder(
3063 SequenceAnnotationOrder annotationSortOrder)
3065 this.annotationSortOrder = annotationSortOrder;
3068 public Map<KeyStroke, JMenuItem> getAccelerators()
3070 return this.accelerators;
3074 * Returns the selected index of the tabbed pane, or -1 if none selected
3075 * (including the case where the tabbed pane has not been made visible).
3079 public int getTabIndex()
3081 return tabbedPane.getSelectedIndex();
3084 public JPanel getStatusPanel()
3090 * Sets a reference to the containing split frame. Also makes the 'toggle
3091 * split view' menu item visible and checked.
3095 public void setSplitFrame(SplitContainerI sf)
3097 this.splitFrame = sf;
3100 this.showComplementMenuItem.setVisible(true);
3101 this.showComplementMenuItem.setState(true);
3105 public SplitContainerI getSplitViewContainer()
3107 return this.splitFrame;
3110 protected void showComplement_actionPerformed(boolean state)