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 JMenu fileMenu = new JMenu();
69 protected JMenuItem closeMenuItem = new JMenuItem();
71 protected JMenu editMenu = new JMenu();
73 protected JMenu viewMenu = new JMenu();
75 protected JMenu annotationsMenu = new JMenu();
77 protected JMenu colourMenu = new JMenu();
79 protected JMenu calculateMenu = new JMenu();
81 protected JMenu webService = new JMenu();
83 protected JMenuItem webServiceNoServices;
85 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
87 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
89 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
91 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
93 protected JMenuItem remove2RightMenuItem = new JMenuItem();
95 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
97 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
99 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
101 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
103 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
105 protected JMenuItem sortIDMenuItem = new JMenuItem();
107 protected JMenuItem sortLengthMenuItem = new JMenuItem();
109 protected JMenuItem sortGroupMenuItem = new JMenuItem();
111 protected JMenu sortByAnnotScore = new JMenu();
113 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
115 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
117 protected JMenuItem PCAMenuItem = new JMenuItem();
119 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
121 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
123 BorderLayout borderLayout1 = new BorderLayout();
125 public JLabel statusBar = new JLabel();
127 protected JMenuItem saveAs = new JMenuItem();
129 protected JMenu outputTextboxMenu = new JMenu();
131 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
133 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
135 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
137 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
139 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
141 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
143 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
145 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
147 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
149 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
151 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
153 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
155 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
157 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
159 // protected JRadioButtonMenuItem covariationColour = new
160 // JRadioButtonMenuItem();
162 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
164 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
166 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
168 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
170 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
172 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
174 JMenuItem htmlMenuItem = new JMenuItem();
176 JMenuItem overviewMenuItem = new JMenuItem();
178 protected JMenuItem undoMenuItem = new JMenuItem();
180 protected JMenuItem redoMenuItem = new JMenuItem();
182 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
184 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
186 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
188 JMenuItem printMenuItem = new JMenuItem();
190 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
192 JMenuItem findMenuItem = new JMenuItem();
194 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
196 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
198 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
200 JMenuItem deleteGroups = new JMenuItem();
202 JMenuItem createGroup = new JMenuItem();
204 JMenuItem unGroup = new JMenuItem();
206 JMenuItem delete = new JMenuItem();
208 JMenuItem copy = new JMenuItem();
210 JMenuItem cut = new JMenuItem();
212 JMenu pasteMenu = new JMenu();
214 JMenuItem pasteNew = new JMenuItem();
216 JMenuItem pasteThis = new JMenuItem();
218 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
220 JMenuItem createPNG = new JMenuItem();
222 JMenuItem createBioJS = new JMenuItem();
224 JMenuItem createSVG = new JMenuItem();
226 protected JMenuItem font = new JMenuItem();
228 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
230 JMenuItem epsFile = new JMenuItem();
232 JMenuItem LoadtreeMenuItem = new JMenuItem();
234 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
236 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
238 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
240 protected JMenuItem modifyPID = new JMenuItem();
242 protected JMenuItem modifyConservation = new JMenuItem();
244 protected JMenu sortByTreeMenu = new JMenu();
246 protected JMenu sort = new JMenu();
248 protected JMenu calculateTree = new JMenu();
250 JMenu jMenu2 = new JMenu();
252 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
254 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
256 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
258 protected ButtonGroup colours = new ButtonGroup();
260 JMenuItem vamsasStore = new JMenuItem();
262 protected JMenuItem showTranslation = new JMenuItem();
264 protected JMenuItem extractScores = new JMenuItem();
266 protected JMenuItem expandAlignment = new JMenuItem();
268 protected JMenu showProducts = new JMenu();
270 public JMenuItem openFeatureSettings = new JMenuItem();
272 JMenuItem fetchSequence = new JMenuItem();
274 JMenuItem annotationColour = new JMenuItem();
276 JMenuItem annotationColumn = new JMenuItem();
278 protected JMenuItem rnahelicesColour = new JMenuItem();
280 JMenuItem associatedData = new JMenuItem();
282 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
284 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
286 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
288 JMenu addSequenceMenu = new JMenu();
290 JMenuItem addFromFile = new JMenuItem();
292 JMenuItem addFromText = new JMenuItem();
294 JMenuItem addFromURL = new JMenuItem();
296 JMenuItem exportAnnotations = new JMenuItem();
298 JMenuItem exportFeatures = new JMenuItem();
300 protected JPanel statusPanel = new JPanel();
302 GridLayout gridLayout1 = new GridLayout();
304 JMenu showMenu = new JMenu();
306 JMenuItem showAllSeqs = new JMenuItem();
308 JMenuItem showAllColumns = new JMenuItem();
310 JMenu hideMenu = new JMenu();
312 JMenuItem hideSelSequences = new JMenuItem();
314 JMenuItem hideSelColumns = new JMenuItem();
316 JMenuItem hideAllButSelection = new JMenuItem();
318 JMenuItem hideAllSelection = new JMenuItem();
320 JMenuItem showAllhidden = new JMenuItem();
322 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
324 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
326 protected JMenuItem showAllAlAnnotations = new JMenuItem();
328 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
330 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
332 protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
334 protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
336 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
338 JMenuItem invertColSel = new JMenuItem();
340 protected JTabbedPane tabbedPane = new JTabbedPane();
342 JMenuItem save = new JMenuItem();
344 protected JMenuItem reload = new JMenuItem();
346 JMenuItem newView = new JMenuItem();
348 JMenuItem textColour = new JMenuItem();
350 protected JMenu formatMenu = new JMenu();
352 JMenu selectMenu = new JMenu();
354 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
356 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
358 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
360 protected JMenuItem gatherViews = new JMenuItem();
362 protected JMenuItem expandViews = new JMenuItem();
364 JMenuItem pageSetup = new JMenuItem();
366 JMenuItem alignmentProperties = new JMenuItem();
368 JMenu tooltipSettingsMenu = new JMenu();
370 private JMenuItem justifyLeftMenuItem = new JMenuItem();
372 private JMenuItem justifyRightMenuItem = new JMenuItem();
374 JMenu autoAnnMenu = new JMenu();
376 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
378 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
380 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
382 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
384 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
386 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
388 protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
390 protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
392 private JMenuItem grpsFromSelection = new JMenuItem();
394 private SequenceAnnotationOrder annotationSortOrder;
396 private boolean showAutoCalculatedAbove = false;
398 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
400 private SplitContainerI splitFrame;
407 setJMenuBar(alignFrameMenuBar);
409 // dynamically fill save as menu with available formats
410 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
412 JMenuItem item = new JMenuItem(
413 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
415 item.addActionListener(new ActionListener()
418 public void actionPerformed(ActionEvent e)
420 outputText_actionPerformed(e);
424 outputTextboxMenu.add(item);
426 } catch (Exception e)
428 System.err.println(e.toString());
431 if (!new jalview.util.Platform().isAMac())
433 closeMenuItem.setMnemonic('C');
434 outputTextboxMenu.setMnemonic('T');
435 undoMenuItem.setMnemonic('Z');
436 redoMenuItem.setMnemonic('0');
437 copy.setMnemonic('C');
438 cut.setMnemonic('U');
439 pasteMenu.setMnemonic('P');
440 reload.setMnemonic('R');
443 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
445 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
446 .getUserColourSchemes().keys();
448 while (userColours.hasMoreElements())
450 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
451 userColours.nextElement().toString());
452 radioItem.setName("USER_DEFINED");
453 radioItem.addMouseListener(new MouseAdapter()
456 public void mousePressed(MouseEvent evt)
458 if (evt.isControlDown()
459 || SwingUtilities.isRightMouseButton(evt))
461 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
463 int option = JOptionPane.showInternalConfirmDialog(
464 jalview.gui.Desktop.desktop,
466 .getString("label.remove_from_default_list"),
468 .getString("label.remove_user_defined_colour"),
469 JOptionPane.YES_NO_OPTION);
470 if (option == JOptionPane.YES_OPTION)
472 jalview.gui.UserDefinedColours
473 .removeColourFromDefaults(radioItem.getText());
474 colourMenu.remove(radioItem);
478 radioItem.addActionListener(new ActionListener()
481 public void actionPerformed(ActionEvent evt)
483 userDefinedColour_actionPerformed(evt);
490 radioItem.addActionListener(new ActionListener()
493 public void actionPerformed(ActionEvent evt)
495 userDefinedColour_actionPerformed(evt);
498 colourMenu.insert(radioItem, 15);
499 colours.add(radioItem);
502 colours.add(noColourmenuItem);
503 colours.add(clustalColour);
504 colours.add(zappoColour);
505 colours.add(taylorColour);
506 colours.add(hydrophobicityColour);
507 colours.add(helixColour);
508 colours.add(strandColour);
509 colours.add(turnColour);
510 colours.add(buriedColour);
511 colours.add(userDefinedColour);
512 colours.add(PIDColour);
513 colours.add(BLOSUM62Colour);
514 colours.add(nucleotideColour);
515 colours.add(purinePyrimidineColour);
516 // colours.add(covariationColour);
517 colours.add(tcoffeeColour);
518 colours.add(RNAInteractionColour);
519 setColourSelected(jalview.bin.Cache.getDefault(
520 Preferences.DEFAULT_COLOUR, "None"));
523 public void setColourSelected(String defaultColour)
526 if (defaultColour != null)
528 int index = ColourSchemeProperty
529 .getColourIndexFromName(defaultColour);
533 case ColourSchemeProperty.CLUSTAL:
534 clustalColour.setSelected(true);
538 case ColourSchemeProperty.BLOSUM:
539 BLOSUM62Colour.setSelected(true);
543 case ColourSchemeProperty.PID:
544 PIDColour.setSelected(true);
548 case ColourSchemeProperty.ZAPPO:
549 zappoColour.setSelected(true);
553 case ColourSchemeProperty.TAYLOR:
554 taylorColour.setSelected(true);
557 case ColourSchemeProperty.HYDROPHOBIC:
558 hydrophobicityColour.setSelected(true);
562 case ColourSchemeProperty.HELIX:
563 helixColour.setSelected(true);
567 case ColourSchemeProperty.STRAND:
568 strandColour.setSelected(true);
572 case ColourSchemeProperty.TURN:
573 turnColour.setSelected(true);
577 case ColourSchemeProperty.BURIED:
578 buriedColour.setSelected(true);
582 case ColourSchemeProperty.NUCLEOTIDE:
583 nucleotideColour.setSelected(true);
587 case ColourSchemeProperty.TCOFFEE:
588 tcoffeeColour.setSelected(true);
591 case ColourSchemeProperty.PURINEPYRIMIDINE:
592 purinePyrimidineColour.setSelected(true);
596 case ColourSchemeProperty.RNAINTERACTION:
597 RNAInteractionColour.setSelected(true);
601 * case ColourSchemeProperty.COVARIATION:
602 * covariationColour.setSelected(true);
606 case ColourSchemeProperty.USER_DEFINED:
607 userDefinedColour.setSelected(true);
610 case ColourSchemeProperty.NONE:
612 noColourmenuItem.setSelected(true);
620 private void jbInit() throws Exception
622 fileMenu.setText(MessageManager.getString("action.file"));
624 saveAs.setText(MessageManager.getString("action.save_as") + "...");
625 ActionListener al = new ActionListener()
628 public void actionPerformed(ActionEvent e)
630 saveAs_actionPerformed(e);
633 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
634 .getDefaultToolkit().getMenuShortcutKeyMask()
635 | KeyEvent.SHIFT_MASK, false);
636 addMenuActionAndAccelerator(keyStroke, saveAs, al);
638 closeMenuItem.setText(MessageManager.getString("action.close"));
639 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
640 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
641 al = new ActionListener()
644 public void actionPerformed(ActionEvent e)
646 closeMenuItem_actionPerformed(false);
649 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
651 editMenu.setText(MessageManager.getString("action.edit"));
652 viewMenu.setText(MessageManager.getString("action.view"));
653 annotationsMenu.setText(MessageManager.getString("action.annotations"));
654 colourMenu.setText(MessageManager.getString("action.colour"));
655 calculateMenu.setText(MessageManager.getString("action.calculate"));
656 webService.setText(MessageManager.getString("action.web_service"));
658 selectAllSequenceMenuItem.setText(MessageManager
659 .getString("action.select_all"));
660 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
661 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
662 al = new ActionListener()
665 public void actionPerformed(ActionEvent e)
667 selectAllSequenceMenuItem_actionPerformed(e);
670 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
672 deselectAllSequenceMenuItem.setText(MessageManager
673 .getString("action.deselect_all"));
674 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
675 al = new ActionListener()
678 public void actionPerformed(ActionEvent e)
680 deselectAllSequenceMenuItem_actionPerformed(e);
683 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
685 invertSequenceMenuItem.setText(MessageManager
686 .getString("action.invert_sequence_selection"));
687 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
688 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
689 al = new ActionListener()
692 public void actionPerformed(ActionEvent e)
694 invertSequenceMenuItem_actionPerformed(e);
697 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
699 grpsFromSelection.setText(MessageManager
700 .getString("action.make_groups_selection"));
701 grpsFromSelection.addActionListener(new ActionListener()
704 public void actionPerformed(ActionEvent e)
706 makeGrpsFromSelection_actionPerformed(e);
709 expandAlignment.setText(MessageManager
710 .getString("action.view_flanking_regions"));
711 expandAlignment.setToolTipText(MessageManager
712 .getString("label.view_flanking_regions"));
713 expandAlignment.addActionListener(new ActionListener()
716 public void actionPerformed(ActionEvent e)
721 remove2LeftMenuItem.setText(MessageManager
722 .getString("action.remove_left"));
723 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
724 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
725 al = new ActionListener()
728 public void actionPerformed(ActionEvent e)
730 remove2LeftMenuItem_actionPerformed(e);
733 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
735 remove2RightMenuItem.setText(MessageManager
736 .getString("action.remove_right"));
737 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
738 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
739 al = new ActionListener()
742 public void actionPerformed(ActionEvent e)
744 remove2RightMenuItem_actionPerformed(e);
747 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
749 removeGappedColumnMenuItem.setText(MessageManager
750 .getString("action.remove_empty_columns"));
751 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
752 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
753 al = new ActionListener()
756 public void actionPerformed(ActionEvent e)
758 removeGappedColumnMenuItem_actionPerformed(e);
761 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
763 removeAllGapsMenuItem.setText(MessageManager
764 .getString("action.remove_all_gaps"));
765 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
766 .getDefaultToolkit().getMenuShortcutKeyMask()
767 | KeyEvent.SHIFT_MASK, false);
768 al = new ActionListener()
771 public void actionPerformed(ActionEvent e)
773 removeAllGapsMenuItem_actionPerformed(e);
776 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
778 justifyLeftMenuItem.setText(MessageManager
779 .getString("action.left_justify_alignment"));
780 justifyLeftMenuItem.addActionListener(new ActionListener()
783 public void actionPerformed(ActionEvent e)
785 justifyLeftMenuItem_actionPerformed(e);
788 justifyRightMenuItem.setText(MessageManager
789 .getString("action.right_justify_alignment"));
790 justifyRightMenuItem.addActionListener(new ActionListener()
793 public void actionPerformed(ActionEvent e)
795 justifyRightMenuItem_actionPerformed(e);
798 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
799 viewBoxesMenuItem.setState(true);
800 viewBoxesMenuItem.addActionListener(new ActionListener()
803 public void actionPerformed(ActionEvent e)
805 viewBoxesMenuItem_actionPerformed(e);
808 viewTextMenuItem.setText(MessageManager.getString("action.text"));
809 viewTextMenuItem.setState(true);
810 viewTextMenuItem.addActionListener(new ActionListener()
813 public void actionPerformed(ActionEvent e)
815 viewTextMenuItem_actionPerformed(e);
818 showNonconservedMenuItem.setText(MessageManager
819 .getString("label.show_non_conversed"));
820 showNonconservedMenuItem.setState(false);
821 showNonconservedMenuItem.addActionListener(new ActionListener()
824 public void actionPerformed(ActionEvent e)
826 showUnconservedMenuItem_actionPerformed(e);
829 sortPairwiseMenuItem.setText(MessageManager
830 .getString("action.by_pairwise_id"));
831 sortPairwiseMenuItem.addActionListener(new ActionListener()
834 public void actionPerformed(ActionEvent e)
836 sortPairwiseMenuItem_actionPerformed(e);
839 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
840 sortIDMenuItem.addActionListener(new ActionListener()
843 public void actionPerformed(ActionEvent e)
845 sortIDMenuItem_actionPerformed(e);
849 .setText(MessageManager.getString("action.by_length"));
850 sortLengthMenuItem.addActionListener(new ActionListener()
853 public void actionPerformed(ActionEvent e)
855 sortLengthMenuItem_actionPerformed(e);
858 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
859 sortGroupMenuItem.addActionListener(new ActionListener()
862 public void actionPerformed(ActionEvent e)
864 sortGroupMenuItem_actionPerformed(e);
868 removeRedundancyMenuItem.setText(MessageManager.getString(
869 "action.remove_redundancy").concat("..."));
870 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
871 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
872 al = new ActionListener()
875 public void actionPerformed(ActionEvent e)
877 removeRedundancyMenuItem_actionPerformed(e);
880 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
882 pairwiseAlignmentMenuItem.setText(MessageManager
883 .getString("action.pairwise_alignment"));
884 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
887 public void actionPerformed(ActionEvent e)
889 pairwiseAlignmentMenuItem_actionPerformed(e);
892 PCAMenuItem.setText(MessageManager
893 .getString("label.principal_component_analysis"));
894 PCAMenuItem.addActionListener(new ActionListener()
897 public void actionPerformed(ActionEvent e)
899 PCAMenuItem_actionPerformed(e);
902 averageDistanceTreeMenuItem.setText(MessageManager
903 .getString("label.average_distance_identity"));
904 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
907 public void actionPerformed(ActionEvent e)
909 averageDistanceTreeMenuItem_actionPerformed(e);
912 neighbourTreeMenuItem.setText(MessageManager
913 .getString("label.neighbour_joining_identity"));
914 neighbourTreeMenuItem.addActionListener(new ActionListener()
917 public void actionPerformed(ActionEvent e)
919 neighbourTreeMenuItem_actionPerformed(e);
922 this.getContentPane().setLayout(borderLayout1);
923 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
924 statusBar.setBackground(Color.white);
925 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
926 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
927 statusBar.setText(MessageManager.getString("label.status_bar"));
928 outputTextboxMenu.setText(MessageManager
929 .getString("label.out_to_textbox"));
930 clustalColour.setText(MessageManager.getString("label.clustalx"));
932 clustalColour.addActionListener(new ActionListener()
935 public void actionPerformed(ActionEvent e)
937 clustalColour_actionPerformed(e);
940 zappoColour.setText(MessageManager.getString("label.zappo"));
941 zappoColour.addActionListener(new ActionListener()
944 public void actionPerformed(ActionEvent e)
946 zappoColour_actionPerformed(e);
949 taylorColour.setText(MessageManager.getString("label.taylor"));
950 taylorColour.addActionListener(new ActionListener()
953 public void actionPerformed(ActionEvent e)
955 taylorColour_actionPerformed(e);
958 hydrophobicityColour.setText(MessageManager
959 .getString("label.hydrophobicity"));
960 hydrophobicityColour.addActionListener(new ActionListener()
963 public void actionPerformed(ActionEvent e)
965 hydrophobicityColour_actionPerformed(e);
968 helixColour.setText(MessageManager.getString("label.helix_propensity"));
969 helixColour.addActionListener(new ActionListener()
972 public void actionPerformed(ActionEvent e)
974 helixColour_actionPerformed(e);
977 strandColour.setText(MessageManager
978 .getString("label.strand_propensity"));
979 strandColour.addActionListener(new ActionListener()
982 public void actionPerformed(ActionEvent e)
984 strandColour_actionPerformed(e);
987 turnColour.setText(MessageManager.getString("label.turn_propensity"));
988 turnColour.addActionListener(new ActionListener()
991 public void actionPerformed(ActionEvent e)
993 turnColour_actionPerformed(e);
996 buriedColour.setText(MessageManager.getString("label.buried_index"));
997 buriedColour.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 buriedColour_actionPerformed(e);
1005 userDefinedColour.setText(MessageManager
1006 .getString("action.user_defined"));
1007 userDefinedColour.addActionListener(new ActionListener()
1010 public void actionPerformed(ActionEvent e)
1012 userDefinedColour_actionPerformed(e);
1016 .setText(MessageManager.getString("label.percentage_identity"));
1017 PIDColour.addActionListener(new ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 PIDColour_actionPerformed(e);
1026 .setText(MessageManager.getString("label.blosum62_score"));
1027 BLOSUM62Colour.addActionListener(new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 BLOSUM62Colour_actionPerformed(e);
1035 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1036 nucleotideColour.addActionListener(new ActionListener()
1039 public void actionPerformed(ActionEvent e)
1041 nucleotideColour_actionPerformed(e);
1045 purinePyrimidineColour.setText(MessageManager
1046 .getString("label.purine_pyrimidine"));
1047 purinePyrimidineColour.addActionListener(new ActionListener()
1050 public void actionPerformed(ActionEvent e)
1052 purinePyrimidineColour_actionPerformed(e);
1056 RNAInteractionColour.setText("RNA Interaction type");
1057 RNAInteractionColour.addActionListener(new ActionListener()
1060 public void actionPerformed(ActionEvent e)
1062 RNAInteractionColour_actionPerformed(e);
1066 * covariationColour.setText("Covariation");
1067 * covariationColour.addActionListener(new ActionListener() { public void
1068 * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
1072 avDistanceTreeBlosumMenuItem.setText(MessageManager
1073 .getString("label.average_distance_bloslum62"));
1074 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
1077 public void actionPerformed(ActionEvent e)
1079 avTreeBlosumMenuItem_actionPerformed(e);
1082 njTreeBlosumMenuItem.setText(MessageManager
1083 .getString("label.neighbour_blosum62"));
1084 njTreeBlosumMenuItem.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1089 njTreeBlosumMenuItem_actionPerformed(e);
1092 annotationPanelMenuItem.setActionCommand("");
1093 annotationPanelMenuItem.setText(MessageManager
1094 .getString("label.show_annotations"));
1095 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1097 annotationPanelMenuItem.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 annotationPanelMenuItem_actionPerformed(e);
1105 showAllAlAnnotations.setText(MessageManager
1106 .getString("label.show_all_al_annotations"));
1107 final boolean isAnnotationPanelShown = annotationPanelMenuItem
1109 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1110 showAllAlAnnotations.addActionListener(new ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 showAllAnnotations_actionPerformed(false, true);
1118 hideAllAlAnnotations.setText(MessageManager
1119 .getString("label.hide_all_al_annotations"));
1120 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1121 hideAllAlAnnotations.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 hideAllAnnotations_actionPerformed(false, true);
1129 showAllSeqAnnotations.setText(MessageManager
1130 .getString("label.show_all_seq_annotations"));
1131 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1132 showAllSeqAnnotations.addActionListener(new ActionListener()
1135 public void actionPerformed(ActionEvent e)
1137 showAllAnnotations_actionPerformed(true, false);
1140 hideAllSeqAnnotations.setText(MessageManager
1141 .getString("label.hide_all_seq_annotations"));
1142 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1143 hideAllSeqAnnotations.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 hideAllAnnotations_actionPerformed(true, false);
1151 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1152 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
1153 SequenceAnnotationOrder.NONE.name()));
1154 sortAnnBySequence.setText(MessageManager
1155 .getString("label.sort_annotations_by_sequence"));
1157 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1158 sortAnnBySequence.addActionListener(new ActionListener()
1161 public void actionPerformed(ActionEvent e)
1163 boolean newState = sortAnnBySequence.getState();
1164 sortAnnByLabel.setSelected(false);
1165 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1166 : SequenceAnnotationOrder.NONE);
1167 sortAnnotations_actionPerformed();
1170 sortAnnByLabel.setText(MessageManager
1171 .getString("label.sort_annotations_by_label"));
1173 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1174 sortAnnByLabel.addActionListener(new ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 boolean newState = sortAnnByLabel.getState();
1180 sortAnnBySequence.setSelected(false);
1181 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1182 : SequenceAnnotationOrder.NONE);
1183 sortAnnotations_actionPerformed();
1186 colourTextMenuItem.setText(MessageManager
1187 .getString("label.colour_text"));
1188 colourTextMenuItem.addActionListener(new ActionListener()
1191 public void actionPerformed(ActionEvent e)
1193 colourTextMenuItem_actionPerformed(e);
1196 htmlMenuItem.setText(MessageManager.getString("label.html"));
1197 htmlMenuItem.addActionListener(new ActionListener()
1200 public void actionPerformed(ActionEvent e)
1202 htmlMenuItem_actionPerformed(e);
1206 // TODO uncomment when supported by MassageManager
1207 // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
1208 createBioJS.setText("BioJS");
1209 createBioJS.addActionListener(new java.awt.event.ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 bioJSMenuItem_actionPerformed(e);
1218 overviewMenuItem.setText(MessageManager
1219 .getString("label.overview_window"));
1220 overviewMenuItem.addActionListener(new ActionListener()
1223 public void actionPerformed(ActionEvent e)
1225 overviewMenuItem_actionPerformed(e);
1229 undoMenuItem.setEnabled(false);
1230 undoMenuItem.setText(MessageManager.getString("action.undo"));
1231 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
1232 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1233 al = new ActionListener()
1236 public void actionPerformed(ActionEvent e)
1238 undoMenuItem_actionPerformed(e);
1241 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
1243 redoMenuItem.setEnabled(false);
1244 redoMenuItem.setText(MessageManager.getString("action.redo"));
1245 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
1246 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1247 al = new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 redoMenuItem_actionPerformed(e);
1255 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
1257 conservationMenuItem.setText(MessageManager
1258 .getString("action.by_conservation"));
1259 conservationMenuItem.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 conservationMenuItem_actionPerformed(e);
1267 noColourmenuItem.setText(MessageManager.getString("label.none"));
1268 noColourmenuItem.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 noColourmenuItem_actionPerformed(e);
1276 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1277 wrapMenuItem.addActionListener(new ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 wrapMenuItem_actionPerformed(e);
1286 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1287 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
1288 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1289 al = new ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 printMenuItem_actionPerformed(e);
1297 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
1300 .setText(MessageManager.getString("action.show_gaps"));
1301 renderGapsMenuItem.setState(true);
1302 renderGapsMenuItem.addActionListener(new ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 renderGapsMenuItem_actionPerformed(e);
1311 findMenuItem.setText(MessageManager.getString("action.find"));
1312 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
1313 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1314 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1315 MessageManager.getString("label.find_tip")));
1316 al = new ActionListener()
1319 public void actionPerformed(ActionEvent e)
1321 findMenuItem_actionPerformed(e);
1324 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
1326 abovePIDThreshold.setText(MessageManager
1327 .getString("label.above_identity_threshold"));
1328 abovePIDThreshold.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 abovePIDThreshold_actionPerformed(e);
1336 showSeqFeatures.setText(MessageManager
1337 .getString("label.show_sequence_features"));
1338 showSeqFeatures.addActionListener(new ActionListener()
1341 public void actionPerformed(ActionEvent actionEvent)
1343 showSeqFeatures_actionPerformed(actionEvent);
1347 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1348 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1349 * void actionPerformed(ActionEvent actionEvent) {
1350 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1352 showDbRefsMenuitem.setText(MessageManager
1353 .getString("label.show_database_refs"));
1354 showDbRefsMenuitem.addActionListener(new ActionListener()
1358 public void actionPerformed(ActionEvent e)
1360 showDbRefs_actionPerformed(e);
1364 showNpFeatsMenuitem.setText(MessageManager
1365 .getString("label.show_non_positional_features"));
1366 showNpFeatsMenuitem.addActionListener(new ActionListener()
1370 public void actionPerformed(ActionEvent e)
1372 showNpFeats_actionPerformed(e);
1376 showGroupConservation.setText(MessageManager
1377 .getString("label.group_conservation"));
1378 showGroupConservation.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 showGroupConservation_actionPerformed(e);
1389 showGroupConsensus.setText(MessageManager
1390 .getString("label.group_consensus"));
1391 showGroupConsensus.addActionListener(new ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 showGroupConsensus_actionPerformed(e);
1401 showConsensusHistogram.setText(MessageManager
1402 .getString("label.show_consensus_histogram"));
1403 showConsensusHistogram.addActionListener(new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 showConsensusHistogram_actionPerformed(e);
1413 showSequenceLogo.setText(MessageManager
1414 .getString("label.show_consensus_logo"));
1415 showSequenceLogo.addActionListener(new ActionListener()
1419 public void actionPerformed(ActionEvent e)
1421 showSequenceLogo_actionPerformed(e);
1425 normaliseSequenceLogo.setText(MessageManager
1426 .getString("label.norm_consensus_logo"));
1427 normaliseSequenceLogo.addActionListener(new ActionListener()
1431 public void actionPerformed(ActionEvent e)
1433 normaliseSequenceLogo_actionPerformed(e);
1437 applyAutoAnnotationSettings.setText(MessageManager
1438 .getString("label.apply_all_groups"));
1439 applyAutoAnnotationSettings.setState(false);
1440 applyAutoAnnotationSettings.setVisible(true);
1441 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1444 public void actionPerformed(ActionEvent e)
1446 applyAutoAnnotationSettings_actionPerformed(e);
1450 ButtonGroup buttonGroup = new ButtonGroup();
1451 buttonGroup.add(showAutoFirst);
1452 buttonGroup.add(showAutoLast);
1453 showAutoFirst.setText(MessageManager.getString("label.show_first"));
1454 showAutoFirst.setSelected(Cache.getDefault(
1455 Preferences.SHOW_AUTOCALC_ABOVE, false));
1456 showAutoFirst.addActionListener(new ActionListener()
1459 public void actionPerformed(ActionEvent e)
1461 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1462 sortAnnotations_actionPerformed();
1465 showAutoLast.setText(MessageManager.getString("label.show_last"));
1466 showAutoLast.setSelected(!showAutoFirst.isSelected());
1467 showAutoLast.addActionListener(new ActionListener()
1470 public void actionPerformed(ActionEvent e)
1472 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1473 sortAnnotations_actionPerformed();
1477 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1478 nucleotideColour.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 nucleotideColour_actionPerformed(e);
1487 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1488 tcoffeeColour.setEnabled(false);
1489 tcoffeeColour.addActionListener(new ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 tcoffeeColorScheme_actionPerformed(e);
1500 .setText(MessageManager.getString("action.undefine_groups"));
1501 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1502 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1503 al = new ActionListener()
1506 public void actionPerformed(ActionEvent e)
1508 deleteGroups_actionPerformed(e);
1511 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1513 createGroup.setText(MessageManager.getString("action.create_groups"));
1514 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1515 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1516 al = new ActionListener()
1519 public void actionPerformed(ActionEvent e)
1521 createGroup_actionPerformed(e);
1524 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1526 unGroup.setText(MessageManager.getString("action.remove_group"));
1527 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1528 .getDefaultToolkit().getMenuShortcutKeyMask()
1529 | KeyEvent.SHIFT_MASK, false);
1530 al = new ActionListener()
1533 public void actionPerformed(ActionEvent e)
1535 unGroup_actionPerformed(e);
1538 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1540 copy.setText(MessageManager.getString("action.copy"));
1541 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1542 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1544 al = new ActionListener()
1547 public void actionPerformed(ActionEvent e)
1549 copy_actionPerformed(e);
1552 addMenuActionAndAccelerator(keyStroke, copy, al);
1554 cut.setText(MessageManager.getString("action.cut"));
1555 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1556 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1557 al = new ActionListener()
1560 public void actionPerformed(ActionEvent e)
1562 cut_actionPerformed(e);
1565 addMenuActionAndAccelerator(keyStroke, cut, al);
1567 delete.setText(MessageManager.getString("action.delete"));
1568 delete.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 delete_actionPerformed(e);
1577 pasteMenu.setText(MessageManager.getString("action.paste"));
1578 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1579 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1580 .getDefaultToolkit().getMenuShortcutKeyMask()
1581 | KeyEvent.SHIFT_MASK, false);
1582 al = new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 pasteNew_actionPerformed(e);
1590 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1592 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1593 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1594 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1595 al = new ActionListener()
1598 public void actionPerformed(ActionEvent e)
1600 pasteThis_actionPerformed(e);
1603 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1605 applyToAllGroups.setText(MessageManager
1606 .getString("label.apply_colour_to_all_groups"));
1607 applyToAllGroups.addActionListener(new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 applyToAllGroups_actionPerformed(e);
1615 createPNG.addActionListener(new ActionListener()
1618 public void actionPerformed(ActionEvent e)
1623 createPNG.setActionCommand(MessageManager
1624 .getString("label.save_png_image"));
1625 createPNG.setText("PNG");
1627 font.setText(MessageManager.getString("action.font"));
1628 font.addActionListener(new ActionListener()
1631 public void actionPerformed(ActionEvent e)
1633 font_actionPerformed(e);
1636 seqLimits.setText(MessageManager
1637 .getString("label.show_sequence_limits"));
1638 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1639 seqLimits.addActionListener(new ActionListener()
1642 public void actionPerformed(ActionEvent e)
1644 seqLimit_actionPerformed(e);
1647 epsFile.setText("EPS");
1648 epsFile.addActionListener(new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1657 createSVG.setText("SVG");
1658 createSVG.addActionListener(new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1667 LoadtreeMenuItem.setActionCommand(MessageManager
1668 .getString("label.load_tree_for_sequence_set"));
1669 LoadtreeMenuItem.setText(MessageManager
1670 .getString("label.load_associated_tree"));
1671 LoadtreeMenuItem.addActionListener(new ActionListener()
1674 public void actionPerformed(ActionEvent e)
1676 LoadtreeMenuItem_actionPerformed(e);
1680 scaleAbove.setVisible(false);
1681 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1682 scaleAbove.addActionListener(new ActionListener()
1685 public void actionPerformed(ActionEvent e)
1687 scaleAbove_actionPerformed(e);
1690 scaleLeft.setVisible(false);
1691 scaleLeft.setSelected(true);
1692 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1693 scaleLeft.addActionListener(new ActionListener()
1696 public void actionPerformed(ActionEvent e)
1698 scaleLeft_actionPerformed(e);
1701 scaleRight.setVisible(false);
1702 scaleRight.setSelected(true);
1703 scaleRight.setText(MessageManager.getString("action.scale_right"));
1704 scaleRight.addActionListener(new ActionListener()
1707 public void actionPerformed(ActionEvent e)
1709 scaleRight_actionPerformed(e);
1712 centreColumnLabelsMenuItem.setVisible(true);
1713 centreColumnLabelsMenuItem.setState(false);
1714 centreColumnLabelsMenuItem.setText(MessageManager
1715 .getString("label.centre_column_labels"));
1716 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1719 public void actionPerformed(ActionEvent e)
1721 centreColumnLabels_actionPerformed(e);
1724 followHighlightMenuItem.setVisible(true);
1725 followHighlightMenuItem.setState(true);
1726 followHighlightMenuItem.setText(MessageManager
1727 .getString("label.automatic_scrolling"));
1728 followHighlightMenuItem.addActionListener(new ActionListener()
1732 public void actionPerformed(ActionEvent e)
1734 followHighlight_actionPerformed();
1739 modifyPID.setText(MessageManager
1740 .getString("label.modify_identity_thereshold"));
1741 modifyPID.addActionListener(new ActionListener()
1744 public void actionPerformed(ActionEvent e)
1746 modifyPID_actionPerformed(e);
1749 modifyConservation.setText(MessageManager
1750 .getString("label.modify_conservation_thereshold"));
1751 modifyConservation.addActionListener(new ActionListener()
1754 public void actionPerformed(ActionEvent e)
1756 modifyConservation_actionPerformed(e);
1760 .setText(MessageManager.getString("action.by_tree_order"));
1761 sort.setText(MessageManager.getString("action.sort"));
1762 sort.addMenuListener(new MenuListener()
1765 public void menuSelected(MenuEvent e)
1771 public void menuDeselected(MenuEvent e)
1776 public void menuCanceled(MenuEvent e)
1780 sortByAnnotScore.setText(MessageManager
1781 .getString("label.sort_by_score"));
1782 sort.add(sortByAnnotScore);
1783 sort.addMenuListener(new javax.swing.event.MenuListener()
1787 public void menuCanceled(MenuEvent e)
1792 public void menuDeselected(MenuEvent e)
1797 public void menuSelected(MenuEvent e)
1799 buildSortByAnnotationScoresMenu();
1802 sortByAnnotScore.setVisible(false);
1805 .setText(MessageManager.getString("action.calculate_tree"));
1807 jMenu2.setText(MessageManager.getString("label.export_image"));
1808 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1809 padGapsMenuitem.setState(jalview.bin.Cache
1810 .getDefault("PAD_GAPS", false));
1811 padGapsMenuitem.addActionListener(new ActionListener()
1814 public void actionPerformed(ActionEvent e)
1816 padGapsMenuitem_actionPerformed(e);
1819 vamsasStore.setVisible(false);
1820 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1821 vamsasStore.addActionListener(new ActionListener()
1824 public void actionPerformed(ActionEvent e)
1826 vamsasStore_actionPerformed(e);
1829 showTranslation.setText(MessageManager
1830 .getString("label.translate_cDNA"));
1831 showTranslation.addActionListener(new ActionListener()
1834 public void actionPerformed(ActionEvent e)
1836 showTranslation_actionPerformed(e);
1840 extractScores.setText(MessageManager.getString("label.extract_scores")
1842 extractScores.addActionListener(new ActionListener()
1845 public void actionPerformed(ActionEvent e)
1847 extractScores_actionPerformed(e);
1850 extractScores.setVisible(true);
1851 // JBPNote: TODO: make gui for regex based score extraction
1853 // for show products actions see AlignFrame.canShowProducts
1854 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1855 openFeatureSettings.setText(MessageManager
1856 .getString("label.feature_settings"));
1857 openFeatureSettings.addActionListener(new ActionListener()
1860 public void actionPerformed(ActionEvent e)
1862 featureSettings_actionPerformed(e);
1866 .setText(MessageManager.getString("label.fetch_sequences"));
1867 fetchSequence.addActionListener(new ActionListener()
1870 public void actionPerformed(ActionEvent e)
1872 fetchSequence_actionPerformed(e);
1876 annotationColour.setText(MessageManager
1877 .getString("action.by_annotation"));
1878 annotationColour.addActionListener(new ActionListener()
1881 public void actionPerformed(ActionEvent e)
1883 annotationColour_actionPerformed(e);
1887 annotationColumn.setText(MessageManager
1888 .getString("action.select_by_annotation"));
1889 annotationColumn.addActionListener(new ActionListener()
1892 public void actionPerformed(ActionEvent e)
1894 annotationColumn_actionPerformed(e);
1898 rnahelicesColour.setText(MessageManager
1899 .getString("action.by_rna_helixes"));
1900 rnahelicesColour.addActionListener(new ActionListener()
1903 public void actionPerformed(ActionEvent e)
1905 rnahelicesColour_actionPerformed(e);
1909 associatedData.setText(MessageManager
1910 .getString("label.load_features_annotations"));
1911 associatedData.addActionListener(new ActionListener()
1914 public void actionPerformed(ActionEvent e)
1916 associatedData_actionPerformed(e);
1919 autoCalculate.setText(MessageManager
1920 .getString("label.autocalculate_consensus"));
1921 autoCalculate.setState(jalview.bin.Cache.getDefault(
1922 "AUTO_CALC_CONSENSUS", true));
1923 autoCalculate.addActionListener(new ActionListener()
1926 public void actionPerformed(ActionEvent e)
1928 autoCalculate_actionPerformed(e);
1931 sortByTree.setText(MessageManager
1932 .getString("label.sort_alignment_new_tree"));
1934 .setToolTipText("<html>"
1936 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1938 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1939 sortByTree.addActionListener(new ActionListener()
1942 public void actionPerformed(ActionEvent e)
1944 sortByTreeOption_actionPerformed(e);
1948 listenToViewSelections.setText(MessageManager
1949 .getString("label.listen_for_selections"));
1950 listenToViewSelections
1951 .setToolTipText("<html>"
1953 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1954 listenToViewSelections.setState(false);
1955 listenToViewSelections.addActionListener(new ActionListener()
1958 public void actionPerformed(ActionEvent e)
1960 listenToViewSelections_actionPerformed(e);
1965 .setText(MessageManager.getString("label.add_sequences"));
1966 addFromFile.setText(MessageManager.getString("label.from_file"));
1967 addFromFile.addActionListener(new ActionListener()
1970 public void actionPerformed(ActionEvent e)
1972 addFromFile_actionPerformed(e);
1975 addFromText.setText(MessageManager.getString("label.from_textbox"));
1976 addFromText.addActionListener(new ActionListener()
1979 public void actionPerformed(ActionEvent e)
1981 addFromText_actionPerformed(e);
1984 addFromURL.setText(MessageManager.getString("label.from_url"));
1985 addFromURL.addActionListener(new ActionListener()
1988 public void actionPerformed(ActionEvent e)
1990 addFromURL_actionPerformed(e);
1993 exportFeatures.setText(MessageManager
1994 .getString("label.export_features"));
1995 exportFeatures.addActionListener(new ActionListener()
1998 public void actionPerformed(ActionEvent e)
2000 exportFeatures_actionPerformed(e);
2003 exportAnnotations.setText(MessageManager
2004 .getString("label.export_annotations"));
2005 exportAnnotations.addActionListener(new ActionListener()
2008 public void actionPerformed(ActionEvent e)
2010 exportAnnotations_actionPerformed(e);
2013 statusPanel.setLayout(gridLayout1);
2014 showMenu.setText(MessageManager.getString("action.show"));
2015 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
2016 showAllSeqs.setToolTipText(MessageManager
2017 .getString("label.toggle_sequence_visibility"));
2018 showAllSeqs.addActionListener(new ActionListener()
2021 public void actionPerformed(ActionEvent e)
2023 showAllSeqs_actionPerformed(e);
2026 showAllColumns.setText(MessageManager.getString("label.all_columns"));
2027 showAllColumns.setToolTipText(MessageManager
2028 .getString("label.toggle_columns_visibility"));
2029 showAllColumns.addActionListener(new ActionListener()
2032 public void actionPerformed(ActionEvent e)
2034 showAllColumns_actionPerformed(e);
2037 hideMenu.setText(MessageManager.getString("action.hide"));
2038 hideSelSequences.setText(MessageManager
2039 .getString("label.selected_sequences"));
2040 hideSelSequences.setToolTipText(MessageManager
2041 .getString("label.toggle_sequence_visibility"));
2042 hideSelSequences.addActionListener(new ActionListener()
2045 public void actionPerformed(ActionEvent e)
2047 hideSelSequences_actionPerformed(e);
2050 hideSelColumns.setText(MessageManager
2051 .getString("label.selected_columns"));
2052 hideSelColumns.setToolTipText(MessageManager
2053 .getString("label.toggle_columns_visibility"));
2054 hideSelColumns.addActionListener(new ActionListener()
2057 public void actionPerformed(ActionEvent e)
2059 hideSelColumns_actionPerformed(e);
2062 hideAllSelection.setText(MessageManager
2063 .getString("label.selected_region"));
2064 hideAllSelection.addActionListener(new ActionListener()
2067 public void actionPerformed(ActionEvent e)
2069 hideAllSelection_actionPerformed(e);
2072 // TODO: should be hidden if no selection exists.
2073 hideAllButSelection.setText(MessageManager
2074 .getString("label.all_but_selected_region"));
2075 hideAllButSelection.addActionListener(new ActionListener()
2078 public void actionPerformed(ActionEvent e)
2080 hideAllButSelection_actionPerformed(e);
2083 showAllhidden.setText(MessageManager
2084 .getString("label.all_sequences_columns"));
2085 showAllhidden.setToolTipText(MessageManager
2086 .getString("label.toggles_visibility_hidden_selected_regions"));
2087 showAllhidden.addActionListener(new ActionListener()
2090 public void actionPerformed(ActionEvent e)
2092 showAllhidden_actionPerformed(e);
2095 hiddenMarkers.setText(MessageManager
2096 .getString("action.show_hidden_markers"));
2097 hiddenMarkers.addActionListener(new ActionListener()
2100 public void actionPerformed(ActionEvent e)
2102 hiddenMarkers_actionPerformed(e);
2106 invertColSel.setText(MessageManager
2107 .getString("action.invert_column_selection"));
2108 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
2109 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
2110 | KeyEvent.ALT_MASK, false);
2111 al = new ActionListener()
2114 public void actionPerformed(ActionEvent e)
2116 invertColSel_actionPerformed(e);
2119 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
2121 showComplementMenuItem.setVisible(false);
2122 showComplementMenuItem.addActionListener(new ActionListener()
2125 public void actionPerformed(ActionEvent e)
2127 showComplement_actionPerformed(showComplementMenuItem.getState());
2131 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2134 public void stateChanged(ChangeEvent evt)
2136 JTabbedPane pane = (JTabbedPane) evt.getSource();
2137 int sel = pane.getSelectedIndex();
2138 tabSelectionChanged(sel);
2141 tabbedPane.addMouseListener(new MouseAdapter()
2144 public void mousePressed(MouseEvent e)
2146 tabbedPane_mousePressed(e);
2149 tabbedPane.addFocusListener(new FocusAdapter()
2152 public void focusGained(FocusEvent e)
2154 tabbedPane_focusGained(e);
2158 save.setText(MessageManager.getString("action.save"));
2159 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
2160 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2161 al = new ActionListener()
2164 public void actionPerformed(ActionEvent e)
2166 save_actionPerformed(e);
2169 addMenuActionAndAccelerator(keyStroke, save, al);
2171 reload.setEnabled(false);
2172 reload.setText(MessageManager.getString("action.reload"));
2173 reload.addActionListener(new ActionListener()
2176 public void actionPerformed(ActionEvent e)
2178 reload_actionPerformed(e);
2182 newView.setText(MessageManager.getString("action.new_view"));
2183 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
2184 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2185 al = new ActionListener()
2188 public void actionPerformed(ActionEvent e)
2190 newView_actionPerformed(e);
2193 addMenuActionAndAccelerator(keyStroke, newView, al);
2195 tabbedPane.setToolTipText("<html><i>"
2196 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2198 textColour.setText(MessageManager.getString("label.colour_text")
2200 textColour.addActionListener(new ActionListener()
2203 public void actionPerformed(ActionEvent e)
2205 textColour_actionPerformed(e);
2208 formatMenu.setText(MessageManager.getString("action.format"));
2209 selectMenu.setText(MessageManager.getString("action.select"));
2210 idRightAlign.setText(MessageManager
2211 .getString("label.right_align_sequence_id"));
2212 idRightAlign.addActionListener(new ActionListener()
2215 public void actionPerformed(ActionEvent e)
2217 idRightAlign_actionPerformed(e);
2221 gatherViews.setEnabled(false);
2222 gatherViews.setText(MessageManager.getString("action.gather_views"));
2223 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
2224 al = new ActionListener()
2227 public void actionPerformed(ActionEvent e)
2229 gatherViews_actionPerformed(e);
2232 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
2234 expandViews.setEnabled(false);
2235 expandViews.setText(MessageManager.getString("action.expand_views"));
2236 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
2237 al = new ActionListener()
2240 public void actionPerformed(ActionEvent e)
2242 expandViews_actionPerformed(e);
2245 addMenuActionAndAccelerator(keyStroke, expandViews, al);
2248 .setText(MessageManager.getString("action.page_setup") + "...");
2249 pageSetup.addActionListener(new ActionListener()
2252 public void actionPerformed(ActionEvent e)
2254 pageSetup_actionPerformed(e);
2257 alignmentProperties.setText(MessageManager
2258 .getString("label.alignment_props") + "...");
2259 alignmentProperties.addActionListener(new ActionListener()
2262 public void actionPerformed(ActionEvent actionEvent)
2264 alignmentProperties();
2267 tooltipSettingsMenu.setText(MessageManager
2268 .getString("label.sequence_id_tooltip"));
2269 autoAnnMenu.setText(MessageManager
2270 .getString("label.autocalculated_annotation"));
2271 alignFrameMenuBar.add(fileMenu);
2272 alignFrameMenuBar.add(editMenu);
2273 alignFrameMenuBar.add(selectMenu);
2274 alignFrameMenuBar.add(viewMenu);
2275 alignFrameMenuBar.add(annotationsMenu);
2276 alignFrameMenuBar.add(formatMenu);
2277 alignFrameMenuBar.add(colourMenu);
2278 alignFrameMenuBar.add(calculateMenu);
2279 alignFrameMenuBar.add(webService);
2280 fileMenu.add(fetchSequence);
2281 fileMenu.add(addSequenceMenu);
2282 fileMenu.add(reload);
2283 fileMenu.addSeparator();
2284 fileMenu.add(vamsasStore);
2286 fileMenu.add(saveAs);
2287 fileMenu.add(outputTextboxMenu);
2288 fileMenu.add(pageSetup);
2289 fileMenu.add(printMenuItem);
2290 fileMenu.addSeparator();
2291 fileMenu.add(jMenu2);
2292 fileMenu.add(exportFeatures);
2293 fileMenu.add(exportAnnotations);
2294 fileMenu.add(LoadtreeMenuItem);
2295 fileMenu.add(associatedData);
2296 fileMenu.addSeparator();
2297 fileMenu.add(closeMenuItem);
2298 editMenu.add(undoMenuItem);
2299 editMenu.add(redoMenuItem);
2302 editMenu.add(pasteMenu);
2303 editMenu.add(delete);
2304 editMenu.addSeparator();
2305 editMenu.add(remove2LeftMenuItem);
2306 editMenu.add(remove2RightMenuItem);
2307 editMenu.add(removeGappedColumnMenuItem);
2308 editMenu.add(removeAllGapsMenuItem);
2309 editMenu.add(removeRedundancyMenuItem);
2310 editMenu.addSeparator();
2311 // dont add these yet in the CVS build - they cannot be undone!
2312 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2313 // editMenu.add(justifyLeftMenuItem);
2314 // editMenu.add(justifyRightMenuItem);
2315 // editMenu.addSeparator();
2316 editMenu.add(padGapsMenuitem);
2317 viewMenu.add(newView);
2318 viewMenu.add(expandViews);
2319 viewMenu.add(gatherViews);
2320 viewMenu.addSeparator();
2321 viewMenu.add(showMenu);
2322 viewMenu.add(hideMenu);
2323 viewMenu.add(showComplementMenuItem);
2324 viewMenu.addSeparator();
2325 viewMenu.add(followHighlightMenuItem);
2326 annotationsMenu.add(annotationPanelMenuItem);
2327 annotationsMenu.addSeparator();
2328 annotationsMenu.add(showAllAlAnnotations);
2329 annotationsMenu.add(hideAllAlAnnotations);
2330 annotationsMenu.addSeparator();
2331 annotationsMenu.add(showAllSeqAnnotations);
2332 annotationsMenu.add(hideAllSeqAnnotations);
2333 annotationsMenu.add(sortAnnBySequence);
2334 annotationsMenu.add(sortAnnByLabel);
2335 annotationsMenu.addSeparator();
2336 autoAnnMenu.add(showAutoFirst);
2337 autoAnnMenu.add(showAutoLast);
2338 autoAnnMenu.addSeparator();
2339 autoAnnMenu.add(applyAutoAnnotationSettings);
2340 autoAnnMenu.add(showConsensusHistogram);
2341 autoAnnMenu.add(showSequenceLogo);
2342 autoAnnMenu.add(normaliseSequenceLogo);
2343 autoAnnMenu.addSeparator();
2344 autoAnnMenu.add(showGroupConservation);
2345 autoAnnMenu.add(showGroupConsensus);
2346 annotationsMenu.add(autoAnnMenu);
2347 viewMenu.addSeparator();
2348 viewMenu.add(showSeqFeatures);
2349 // viewMenu.add(showSeqFeaturesHeight);
2351 viewMenu.add(openFeatureSettings);
2352 tooltipSettingsMenu.add(showDbRefsMenuitem);
2353 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2354 viewMenu.add(tooltipSettingsMenu);
2355 viewMenu.addSeparator();
2356 viewMenu.add(alignmentProperties);
2357 viewMenu.addSeparator();
2358 viewMenu.add(overviewMenuItem);
2359 colourMenu.add(applyToAllGroups);
2360 colourMenu.add(textColour);
2361 colourMenu.addSeparator();
2362 colourMenu.add(noColourmenuItem);
2363 colourMenu.add(clustalColour);
2364 colourMenu.add(BLOSUM62Colour);
2365 colourMenu.add(PIDColour);
2366 colourMenu.add(zappoColour);
2367 colourMenu.add(taylorColour);
2368 colourMenu.add(hydrophobicityColour);
2369 colourMenu.add(helixColour);
2370 colourMenu.add(strandColour);
2371 colourMenu.add(turnColour);
2372 colourMenu.add(buriedColour);
2373 colourMenu.add(nucleotideColour);
2374 colourMenu.add(purinePyrimidineColour);
2375 colourMenu.add(RNAInteractionColour);
2376 // colourMenu.add(covariationColour);
2377 colourMenu.add(tcoffeeColour);
2378 colourMenu.add(userDefinedColour);
2379 colourMenu.addSeparator();
2380 colourMenu.add(conservationMenuItem);
2381 colourMenu.add(modifyConservation);
2382 colourMenu.add(abovePIDThreshold);
2383 colourMenu.add(modifyPID);
2384 colourMenu.add(annotationColour);
2385 colourMenu.add(rnahelicesColour);
2386 calculateMenu.add(sort);
2387 calculateMenu.add(calculateTree);
2388 calculateMenu.addSeparator();
2389 calculateMenu.add(pairwiseAlignmentMenuItem);
2390 calculateMenu.add(PCAMenuItem);
2391 calculateMenu.addSeparator();
2392 calculateMenu.add(showTranslation);
2393 calculateMenu.add(showProducts);
2394 calculateMenu.add(autoCalculate);
2395 calculateMenu.add(sortByTree);
2396 calculateMenu.addSeparator();
2397 calculateMenu.add(extractScores);
2398 webServiceNoServices = new JMenuItem(
2399 MessageManager.getString("label.no_services"));
2400 webService.add(webServiceNoServices);
2401 pasteMenu.add(pasteNew);
2402 pasteMenu.add(pasteThis);
2403 sort.add(sortIDMenuItem);
2404 sort.add(sortLengthMenuItem);
2405 sort.add(sortGroupMenuItem);
2406 sort.add(sortPairwiseMenuItem);
2407 sort.add(sortByTreeMenu);
2408 jMenu2.add(htmlMenuItem);
2409 jMenu2.add(epsFile);
2410 jMenu2.add(createPNG);
2411 jMenu2.add(createBioJS);
2412 jMenu2.add(createSVG);
2413 addSequenceMenu.add(addFromFile);
2414 addSequenceMenu.add(addFromText);
2415 addSequenceMenu.add(addFromURL);
2416 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2417 statusPanel.add(statusBar, null);
2418 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2419 showMenu.add(showAllColumns);
2420 showMenu.add(showAllSeqs);
2421 showMenu.add(showAllhidden);
2422 hideMenu.add(hideSelColumns);
2423 hideMenu.add(hideSelSequences);
2424 hideMenu.add(hideAllSelection);
2425 hideMenu.add(hideAllButSelection);
2427 formatMenu.add(font);
2428 formatMenu.addSeparator();
2429 formatMenu.add(wrapMenuItem);
2430 formatMenu.add(scaleAbove);
2431 formatMenu.add(scaleLeft);
2432 formatMenu.add(scaleRight);
2433 formatMenu.add(seqLimits);
2434 formatMenu.add(idRightAlign);
2435 formatMenu.add(hiddenMarkers);
2436 formatMenu.add(viewBoxesMenuItem);
2437 formatMenu.add(viewTextMenuItem);
2438 formatMenu.add(colourTextMenuItem);
2439 formatMenu.add(renderGapsMenuItem);
2440 formatMenu.add(centreColumnLabelsMenuItem);
2441 formatMenu.add(showNonconservedMenuItem);
2442 selectMenu.add(findMenuItem);
2443 selectMenu.addSeparator();
2444 selectMenu.add(selectAllSequenceMenuItem);
2445 selectMenu.add(deselectAllSequenceMenuItem);
2446 selectMenu.add(invertSequenceMenuItem);
2447 selectMenu.add(invertColSel);
2448 selectMenu.add(createGroup);
2449 selectMenu.add(unGroup);
2450 selectMenu.add(grpsFromSelection);
2451 selectMenu.add(deleteGroups);
2452 selectMenu.add(annotationColumn);
2453 calculateMenu.add(expandAlignment);
2454 // TODO - determine if the listenToViewSelections button is needed : see bug
2456 // selectMenu.addSeparator();
2457 // selectMenu.add(listenToViewSelections);
2461 * Adds the given action listener and key accelerator to the given menu item.
2462 * Also saves in a lookup table to support lookup of action by key stroke.
2466 * @param actionListener
2468 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2469 JMenuItem menuItem, ActionListener actionListener)
2471 menuItem.setAccelerator(keyStroke);
2472 accelerators.put(keyStroke, menuItem);
2473 menuItem.addActionListener(actionListener);
2477 * Action on clicking sort annotations by type.
2481 protected void sortAnnotations_actionPerformed()
2486 * Action on clicking Show all annotations.
2488 * @param forSequences
2489 * update sequence-related annotations
2490 * @param forAlignment
2491 * update non-sequence-related annotations
2493 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2494 boolean forAlignment)
2496 setAnnotationsVisibility(true, forSequences, forAlignment);
2500 * Action on clicking Hide all annotations.
2502 * @param forSequences
2503 * update sequence-related annotations
2504 * @param forAlignment
2505 * update non-sequence-related annotations
2507 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2508 boolean forAlignment)
2510 setAnnotationsVisibility(false, forSequences, forAlignment);
2514 * Set the visibility of annotations to true or false. Can act on
2515 * sequence-related annotations, or alignment-related, or both.
2518 * @param forSequences
2519 * update sequence-related annotations
2520 * @param forAlignment
2521 * update non-sequence-related annotations
2523 protected void setAnnotationsVisibility(boolean visible,
2524 boolean forSequences, boolean forAlignment)
2529 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2531 // TODO Auto-generated method stub
2535 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2537 // TODO Auto-generated method stub
2541 protected void showAllhidden_actionPerformed(ActionEvent e)
2543 // TODO Auto-generated method stub
2547 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2549 // TODO Auto-generated method stub
2553 protected void hideAllSelection_actionPerformed(ActionEvent e)
2555 // TODO Auto-generated method stub
2559 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2561 // TODO Auto-generated method stub
2565 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2567 // TODO Auto-generated method stub
2571 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2573 // TODO Auto-generated method stub
2577 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2579 // TODO Auto-generated method stub
2583 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2585 // TODO Auto-generated method stub
2589 protected void showGroupConservation_actionPerformed(ActionEvent e)
2591 // TODO Auto-generated method stub
2595 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2597 // TODO Auto-generated method stub
2601 protected void showSeqFeaturesHeight_actionPerformed(
2602 ActionEvent actionEvent)
2604 // TODO Auto-generated method stub
2608 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2610 // TODO Auto-generated method stub
2614 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2616 // TODO Auto-generated method stub
2620 protected void followHighlight_actionPerformed()
2622 // TODO Auto-generated method stub
2626 protected void showNpFeats_actionPerformed(ActionEvent e)
2628 // TODO Auto-generated method stub
2632 protected void showDbRefs_actionPerformed(ActionEvent e)
2634 // TODO Auto-generated method stub
2638 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2642 protected void buildSortByAnnotationScoresMenu()
2646 protected void extractScores_actionPerformed(ActionEvent e)
2650 protected void outputText_actionPerformed(ActionEvent e)
2654 public void addFromFile_actionPerformed(ActionEvent e)
2659 public void addFromText_actionPerformed(ActionEvent e)
2664 public void addFromURL_actionPerformed(ActionEvent e)
2669 public void exportFeatures_actionPerformed(ActionEvent e)
2674 public void exportAnnotations_actionPerformed(ActionEvent e)
2679 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2683 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2688 protected void closeMenuItem_actionPerformed(boolean b)
2692 protected void redoMenuItem_actionPerformed(ActionEvent e)
2696 protected void undoMenuItem_actionPerformed(ActionEvent e)
2700 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2704 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2708 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2712 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2716 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2720 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2724 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2728 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2732 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2736 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2740 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2744 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2748 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2752 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2756 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2760 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2764 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2768 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2772 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2776 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2780 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2784 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2788 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2792 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2796 protected void clustalColour_actionPerformed(ActionEvent e)
2800 protected void zappoColour_actionPerformed(ActionEvent e)
2804 protected void taylorColour_actionPerformed(ActionEvent e)
2808 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2812 protected void helixColour_actionPerformed(ActionEvent e)
2816 protected void strandColour_actionPerformed(ActionEvent e)
2820 protected void turnColour_actionPerformed(ActionEvent e)
2824 protected void buriedColour_actionPerformed(ActionEvent e)
2828 protected void userDefinedColour_actionPerformed(ActionEvent e)
2832 protected void PIDColour_actionPerformed(ActionEvent e)
2836 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2840 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2844 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2849 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2852 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2856 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2860 protected void printMenuItem_actionPerformed(ActionEvent e)
2864 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2868 protected void findMenuItem_actionPerformed(ActionEvent e)
2872 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2876 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2880 protected void nucleotideColour_actionPerformed(ActionEvent e)
2884 protected void deleteGroups_actionPerformed(ActionEvent e)
2888 protected void createGroup_actionPerformed(ActionEvent e)
2892 protected void unGroup_actionPerformed(ActionEvent e)
2896 protected void copy_actionPerformed(ActionEvent e)
2900 protected void cut_actionPerformed(ActionEvent e)
2904 protected void delete_actionPerformed(ActionEvent e)
2908 protected void pasteNew_actionPerformed(ActionEvent e)
2912 protected void pasteThis_actionPerformed(ActionEvent e)
2916 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2920 public void createPNG(java.io.File f)
2924 protected void font_actionPerformed(ActionEvent e)
2928 protected void seqLimit_actionPerformed(ActionEvent e)
2932 public void seqDBRef_actionPerformed(ActionEvent e)
2937 public void createEPS(java.io.File f)
2941 public void createSVG(java.io.File f)
2945 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2951 * Template method to handle the 'load T-Coffee scores' menu event.
2953 * Subclasses override this method to provide a custom action.
2958 protected void loadScores_actionPerformed(ActionEvent event)
2964 * Template method to handle the 'Color T-Coffee scores' menu event.
2966 * Subclasses override this method to provide a custom action.
2971 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2976 protected void jpred_actionPerformed(ActionEvent e)
2980 protected void scaleAbove_actionPerformed(ActionEvent e)
2984 protected void scaleLeft_actionPerformed(ActionEvent e)
2988 protected void scaleRight_actionPerformed(ActionEvent e)
2992 protected void modifyPID_actionPerformed(ActionEvent e)
2996 protected void modifyConservation_actionPerformed(ActionEvent e)
3000 protected void saveAs_actionPerformed(ActionEvent e)
3004 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
3008 public void vamsasStore_actionPerformed(ActionEvent e)
3013 public void vamsasLoad_actionPerformed(ActionEvent e)
3018 public void showTranslation_actionPerformed(ActionEvent e)
3023 public void featureSettings_actionPerformed(ActionEvent e)
3028 public void fetchSequence_actionPerformed(ActionEvent e)
3033 public void smoothFont_actionPerformed(ActionEvent e)
3038 public void annotationColour_actionPerformed(ActionEvent e)
3043 public void annotationColumn_actionPerformed(ActionEvent e)
3048 public void rnahelicesColour_actionPerformed(ActionEvent e)
3053 public void associatedData_actionPerformed(ActionEvent e)
3058 public void autoCalculate_actionPerformed(ActionEvent e)
3063 public void sortByTreeOption_actionPerformed(ActionEvent e)
3068 public void showAllSeqs_actionPerformed(ActionEvent e)
3073 public void showAllColumns_actionPerformed(ActionEvent e)
3078 public void hideSelSequences_actionPerformed(ActionEvent e)
3083 public void hideSelColumns_actionPerformed(ActionEvent e)
3088 public void hiddenMarkers_actionPerformed(ActionEvent e)
3093 public void findPdbId_actionPerformed(ActionEvent e)
3098 public void enterPdbId_actionPerformed(ActionEvent e)
3103 public void pdbFile_actionPerformed(ActionEvent e)
3108 public void invertColSel_actionPerformed(ActionEvent e)
3113 public void tabSelectionChanged(int sel)
3118 public void tabbedPane_mousePressed(MouseEvent e)
3123 public void tabbedPane_focusGained(FocusEvent e)
3128 public void save_actionPerformed(ActionEvent e)
3133 public void reload_actionPerformed(ActionEvent e)
3138 public void newView_actionPerformed(ActionEvent e)
3143 public void textColour_actionPerformed(ActionEvent e)
3148 public void idRightAlign_actionPerformed(ActionEvent e)
3153 public void expandViews_actionPerformed(ActionEvent e)
3158 public void gatherViews_actionPerformed(ActionEvent e)
3163 public void buildTreeMenu()
3168 public void pageSetup_actionPerformed(ActionEvent e)
3173 public void alignmentProperties()
3178 protected void expand_newalign(ActionEvent e)
3180 // TODO Auto-generated method stub
3184 protected boolean isShowAutoCalculatedAbove()
3186 return showAutoCalculatedAbove;
3189 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3191 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3194 protected SequenceAnnotationOrder getAnnotationSortOrder()
3196 return annotationSortOrder;
3199 protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3201 this.annotationSortOrder = annotationSortOrder;
3204 public Map<KeyStroke, JMenuItem> getAccelerators()
3206 return this.accelerators;
3210 * Returns the selected index of the tabbed pane, or -1 if none selected
3211 * (including the case where the tabbed pane has not been made visible).
3215 public int getTabIndex()
3217 return tabbedPane.getSelectedIndex();
3220 public JPanel getStatusPanel()
3226 * Sets a reference to the containing split frame. Also makes the 'toggle
3227 * split view' menu item visible and checked.
3231 public void setSplitFrame(SplitContainerI sf)
3233 this.splitFrame = sf;
3236 this.showComplementMenuItem.setVisible(true);
3237 this.showComplementMenuItem.setState(true);
3241 public SplitContainerI getSplitViewContainer()
3243 return this.splitFrame;
3246 protected void showComplement_actionPerformed(boolean state)