2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.bin.Cache;
25 import jalview.gui.JvSwingUtils;
26 import jalview.gui.Preferences;
27 import jalview.schemes.ColourSchemeProperty;
28 import jalview.util.MessageManager;
30 import java.awt.BorderLayout;
31 import java.awt.Color;
32 import java.awt.GridLayout;
33 import java.awt.Toolkit;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.FocusAdapter;
37 import java.awt.event.FocusEvent;
38 import java.awt.event.KeyEvent;
39 import java.awt.event.MouseAdapter;
40 import java.awt.event.MouseEvent;
41 import java.util.HashMap;
44 import javax.swing.BorderFactory;
45 import javax.swing.ButtonGroup;
46 import javax.swing.JCheckBoxMenuItem;
47 import javax.swing.JInternalFrame;
48 import javax.swing.JLabel;
49 import javax.swing.JMenu;
50 import javax.swing.JMenuBar;
51 import javax.swing.JMenuItem;
52 import javax.swing.JOptionPane;
53 import javax.swing.JPanel;
54 import javax.swing.JRadioButtonMenuItem;
55 import javax.swing.JTabbedPane;
56 import javax.swing.KeyStroke;
57 import javax.swing.SwingUtilities;
58 import javax.swing.event.ChangeEvent;
59 import javax.swing.event.MenuEvent;
60 import javax.swing.event.MenuListener;
62 public class GAlignFrame extends JInternalFrame
64 protected JMenuBar alignFrameMenuBar = new JMenuBar();
66 protected JMenu fileMenu = new JMenu();
68 protected JMenuItem closeMenuItem = new JMenuItem();
70 protected JMenu editMenu = new JMenu();
72 protected JMenu viewMenu = new JMenu();
74 protected JMenu annotationsMenu = new JMenu();
76 protected JMenu colourMenu = new JMenu();
78 protected JMenu calculateMenu = new JMenu();
80 protected JMenu webService = new JMenu();
82 protected JMenuItem webServiceNoServices;
84 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
86 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
88 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
90 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
92 protected JMenuItem remove2RightMenuItem = new JMenuItem();
94 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
96 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
98 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
100 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
102 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
104 protected JMenuItem sortIDMenuItem = new JMenuItem();
106 protected JMenuItem sortLengthMenuItem = new JMenuItem();
108 protected JMenuItem sortGroupMenuItem = new JMenuItem();
110 protected JMenu sortByAnnotScore = new JMenu();
112 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
114 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
116 protected JMenuItem PCAMenuItem = new JMenuItem();
118 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
120 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
122 BorderLayout borderLayout1 = new BorderLayout();
124 public JLabel statusBar = new JLabel();
126 protected JMenuItem saveAs = new JMenuItem();
128 protected JMenu outputTextboxMenu = new JMenu();
130 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
144 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
146 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
148 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
150 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
152 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
154 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
156 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
158 // protected JRadioButtonMenuItem covariationColour = new
159 // JRadioButtonMenuItem();
161 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
163 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
165 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
167 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
169 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
171 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
173 JMenuItem htmlMenuItem = new JMenuItem();
175 JMenuItem overviewMenuItem = new JMenuItem();
177 protected JMenuItem undoMenuItem = new JMenuItem();
179 protected JMenuItem redoMenuItem = new JMenuItem();
181 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
183 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
185 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
187 JMenuItem printMenuItem = new JMenuItem();
189 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
191 JMenuItem findMenuItem = new JMenuItem();
193 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
195 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
197 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
199 JMenuItem deleteGroups = new JMenuItem();
201 JMenuItem createGroup = new JMenuItem();
203 JMenuItem unGroup = new JMenuItem();
205 JMenuItem delete = new JMenuItem();
207 JMenuItem copy = new JMenuItem();
209 JMenuItem cut = new JMenuItem();
211 JMenu pasteMenu = new JMenu();
213 JMenuItem pasteNew = new JMenuItem();
215 JMenuItem pasteThis = new JMenuItem();
217 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
219 JMenuItem createPNG = new JMenuItem();
221 JMenuItem createSVG = new JMenuItem();
223 protected JMenuItem font = new JMenuItem();
225 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
227 JMenuItem epsFile = new JMenuItem();
229 JMenuItem LoadtreeMenuItem = new JMenuItem();
231 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
233 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
235 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
237 protected JMenuItem modifyPID = new JMenuItem();
239 protected JMenuItem modifyConservation = new JMenuItem();
241 protected JMenu sortByTreeMenu = new JMenu();
243 protected JMenu sort = new JMenu();
245 protected JMenu calculateTree = new JMenu();
247 JMenu jMenu2 = new JMenu();
249 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
251 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
253 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
255 protected ButtonGroup colours = new ButtonGroup();
257 JMenuItem vamsasStore = new JMenuItem();
259 protected JMenuItem showTranslation = new JMenuItem();
261 protected JMenu cdna = new JMenu();
263 protected JMenuItem extractScores = new JMenuItem();
265 protected JMenuItem expandAlignment = new JMenuItem();
267 protected JMenu showProducts = new JMenu();
269 public JMenuItem openFeatureSettings = new JMenuItem();
271 JMenuItem fetchSequence = new JMenuItem();
273 JMenuItem annotationColour = new JMenuItem();
275 protected JMenuItem rnahelicesColour = new JMenuItem();
277 JMenuItem associatedData = new JMenuItem();
279 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
281 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
283 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
285 JMenu addSequenceMenu = new JMenu();
287 JMenuItem addFromFile = new JMenuItem();
289 JMenuItem addFromText = new JMenuItem();
291 JMenuItem addFromURL = new JMenuItem();
293 JMenuItem exportAnnotations = new JMenuItem();
295 JMenuItem exportFeatures = new JMenuItem();
297 protected JPanel statusPanel = new JPanel();
299 GridLayout gridLayout1 = new GridLayout();
301 JMenu jMenu3 = new JMenu();
303 JMenuItem showAllSeqs = new JMenuItem();
305 JMenuItem showAllColumns = new JMenuItem();
307 JMenu hideMenu = new JMenu();
309 JMenuItem hideSelSequences = new JMenuItem();
311 JMenuItem hideSelColumns = new JMenuItem();
313 JMenuItem hideAllButSelection = new JMenuItem();
315 JMenuItem hideAllSelection = new JMenuItem();
317 JMenuItem showAllhidden = new JMenuItem();
319 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
321 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
323 protected JMenuItem showAllAlAnnotations = new JMenuItem();
325 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
327 protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
329 protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
331 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
333 JMenuItem invertColSel = new JMenuItem();
335 protected JTabbedPane tabbedPane = new JTabbedPane();
337 JMenuItem save = new JMenuItem();
339 protected JMenuItem reload = new JMenuItem();
341 JMenuItem newView = new JMenuItem();
343 JMenuItem textColour = new JMenuItem();
345 JMenu formatMenu = new JMenu();
347 JMenu selectMenu = new JMenu();
349 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
351 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
353 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
355 protected JMenuItem gatherViews = new JMenuItem();
357 protected JMenuItem expandViews = new JMenuItem();
359 JMenuItem pageSetup = new JMenuItem();
361 JMenuItem alignmentProperties = new JMenuItem();
363 JMenu tooltipSettingsMenu = new JMenu();
365 private JMenuItem justifyLeftMenuItem = new JMenuItem();
367 private JMenuItem justifyRightMenuItem = new JMenuItem();
369 JMenu autoAnnMenu = new JMenu();
371 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
373 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
375 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
377 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
379 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
381 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
383 protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
385 protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
387 private JMenuItem grpsFromSelection = new JMenuItem();
389 private SequenceAnnotationOrder annotationSortOrder;
391 private boolean showAutoCalculatedAbove = false;
393 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
400 setJMenuBar(alignFrameMenuBar);
402 // dynamically fill save as menu with available formats
403 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
405 JMenuItem item = new JMenuItem(
406 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
408 item.addActionListener(new ActionListener()
411 public void actionPerformed(ActionEvent e)
413 outputText_actionPerformed(e);
417 outputTextboxMenu.add(item);
419 } catch (Exception e)
421 System.err.println(e.toString());
424 if (!new jalview.util.Platform().isAMac())
426 closeMenuItem.setMnemonic('C');
427 outputTextboxMenu.setMnemonic('T');
428 undoMenuItem.setMnemonic('Z');
429 redoMenuItem.setMnemonic('0');
430 copy.setMnemonic('C');
431 cut.setMnemonic('U');
432 pasteMenu.setMnemonic('P');
433 reload.setMnemonic('R');
436 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
438 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
439 .getUserColourSchemes().keys();
441 while (userColours.hasMoreElements())
443 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
444 userColours.nextElement().toString());
445 radioItem.setName("USER_DEFINED");
446 radioItem.addMouseListener(new MouseAdapter()
449 public void mousePressed(MouseEvent evt)
451 if (evt.isControlDown()
452 || SwingUtilities.isRightMouseButton(evt))
454 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
456 int option = JOptionPane.showInternalConfirmDialog(
457 jalview.gui.Desktop.desktop,
459 .getString("label.remove_from_default_list"),
461 .getString("label.remove_user_defined_colour"),
462 JOptionPane.YES_NO_OPTION);
463 if (option == JOptionPane.YES_OPTION)
465 jalview.gui.UserDefinedColours
466 .removeColourFromDefaults(radioItem.getText());
467 colourMenu.remove(radioItem);
471 radioItem.addActionListener(new ActionListener()
474 public void actionPerformed(ActionEvent evt)
476 userDefinedColour_actionPerformed(evt);
483 radioItem.addActionListener(new ActionListener()
486 public void actionPerformed(ActionEvent evt)
488 userDefinedColour_actionPerformed(evt);
491 colourMenu.insert(radioItem, 15);
492 colours.add(radioItem);
495 colours.add(noColourmenuItem);
496 colours.add(clustalColour);
497 colours.add(zappoColour);
498 colours.add(taylorColour);
499 colours.add(hydrophobicityColour);
500 colours.add(helixColour);
501 colours.add(strandColour);
502 colours.add(turnColour);
503 colours.add(buriedColour);
504 colours.add(userDefinedColour);
505 colours.add(PIDColour);
506 colours.add(BLOSUM62Colour);
507 colours.add(nucleotideColour);
508 colours.add(purinePyrimidineColour);
509 // colours.add(covariationColour);
510 colours.add(tcoffeeColour);
511 colours.add(RNAInteractionColour);
512 setColourSelected(jalview.bin.Cache
513 .getDefault("DEFAULT_COLOUR", "None"));
517 public void setColourSelected(String defaultColour)
520 if (defaultColour != null)
522 int index = ColourSchemeProperty
523 .getColourIndexFromName(defaultColour);
527 case ColourSchemeProperty.CLUSTAL:
528 clustalColour.setSelected(true);
532 case ColourSchemeProperty.BLOSUM:
533 BLOSUM62Colour.setSelected(true);
537 case ColourSchemeProperty.PID:
538 PIDColour.setSelected(true);
542 case ColourSchemeProperty.ZAPPO:
543 zappoColour.setSelected(true);
547 case ColourSchemeProperty.TAYLOR:
548 taylorColour.setSelected(true);
551 case ColourSchemeProperty.HYDROPHOBIC:
552 hydrophobicityColour.setSelected(true);
556 case ColourSchemeProperty.HELIX:
557 helixColour.setSelected(true);
561 case ColourSchemeProperty.STRAND:
562 strandColour.setSelected(true);
566 case ColourSchemeProperty.TURN:
567 turnColour.setSelected(true);
571 case ColourSchemeProperty.BURIED:
572 buriedColour.setSelected(true);
576 case ColourSchemeProperty.NUCLEOTIDE:
577 nucleotideColour.setSelected(true);
581 case ColourSchemeProperty.TCOFFEE:
582 tcoffeeColour.setSelected(true);
585 case ColourSchemeProperty.PURINEPYRIMIDINE:
586 purinePyrimidineColour.setSelected(true);
590 case ColourSchemeProperty.RNAINTERACTION:
591 RNAInteractionColour.setSelected(true);
595 * case ColourSchemeProperty.COVARIATION:
596 * covariationColour.setSelected(true);
600 case ColourSchemeProperty.USER_DEFINED:
601 userDefinedColour.setSelected(true);
604 case ColourSchemeProperty.NONE:
606 noColourmenuItem.setSelected(true);
614 private void jbInit() throws Exception
616 fileMenu.setText(MessageManager.getString("action.file"));
618 saveAs.setText(MessageManager.getString("action.save_as") + "...");
619 ActionListener al = new ActionListener()
622 public void actionPerformed(ActionEvent e)
624 saveAs_actionPerformed(e);
627 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
628 .getDefaultToolkit().getMenuShortcutKeyMask()
629 | KeyEvent.SHIFT_MASK, false);
630 addMenuActionAndAccelerator(keyStroke, saveAs, al);
632 closeMenuItem.setText(MessageManager.getString("action.close"));
633 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
634 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
635 al = new ActionListener()
638 public void actionPerformed(ActionEvent e)
640 closeMenuItem_actionPerformed(false);
643 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
645 editMenu.setText(MessageManager.getString("action.edit"));
646 viewMenu.setText(MessageManager.getString("action.view"));
647 annotationsMenu.setText(MessageManager.getString("action.annotations"));
648 colourMenu.setText(MessageManager.getString("action.colour"));
649 calculateMenu.setText(MessageManager.getString("action.calculate"));
650 webService.setText(MessageManager.getString("action.web_service"));
652 selectAllSequenceMenuItem.setText(MessageManager
653 .getString("action.select_all"));
654 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
655 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
656 al = new ActionListener()
659 public void actionPerformed(ActionEvent e)
661 selectAllSequenceMenuItem_actionPerformed(e);
664 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
666 deselectAllSequenceMenuItem.setText(MessageManager
667 .getString("action.deselect_all"));
668 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
669 al = new ActionListener()
672 public void actionPerformed(ActionEvent e)
674 deselectAllSequenceMenuItem_actionPerformed(e);
677 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
679 invertSequenceMenuItem.setText(MessageManager
680 .getString("action.invert_sequence_selection"));
681 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
682 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
683 al = new ActionListener()
686 public void actionPerformed(ActionEvent e)
688 invertSequenceMenuItem_actionPerformed(e);
691 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
693 grpsFromSelection.setText(MessageManager
694 .getString("action.make_groups_selection"));
695 grpsFromSelection.addActionListener(new ActionListener()
698 public void actionPerformed(ActionEvent e)
700 makeGrpsFromSelection_actionPerformed(e);
703 expandAlignment.setText(MessageManager
704 .getString("action.view_flanking_regions"));
705 expandAlignment.setToolTipText(MessageManager
706 .getString("label.view_flanking_regions"));
707 expandAlignment.addActionListener(new ActionListener()
710 public void actionPerformed(ActionEvent e)
715 remove2LeftMenuItem.setText(MessageManager
716 .getString("action.remove_left"));
717 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
718 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
719 al = new ActionListener()
722 public void actionPerformed(ActionEvent e)
724 remove2LeftMenuItem_actionPerformed(e);
727 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
729 remove2RightMenuItem.setText(MessageManager
730 .getString("action.remove_right"));
731 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
732 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
733 al = new ActionListener()
736 public void actionPerformed(ActionEvent e)
738 remove2RightMenuItem_actionPerformed(e);
741 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
743 removeGappedColumnMenuItem.setText(MessageManager
744 .getString("action.remove_empty_columns"));
745 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
746 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
747 al = new ActionListener()
750 public void actionPerformed(ActionEvent e)
752 removeGappedColumnMenuItem_actionPerformed(e);
755 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
757 removeAllGapsMenuItem.setText(MessageManager
758 .getString("action.remove_all_gaps"));
759 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
760 .getDefaultToolkit().getMenuShortcutKeyMask()
761 | KeyEvent.SHIFT_MASK, false);
762 al = new ActionListener()
765 public void actionPerformed(ActionEvent e)
767 removeAllGapsMenuItem_actionPerformed(e);
770 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
772 justifyLeftMenuItem.setText(MessageManager
773 .getString("action.left_justify_alignment"));
774 justifyLeftMenuItem.addActionListener(new ActionListener()
777 public void actionPerformed(ActionEvent e)
779 justifyLeftMenuItem_actionPerformed(e);
782 justifyRightMenuItem.setText(MessageManager
783 .getString("action.right_justify_alignment"));
784 justifyRightMenuItem.addActionListener(new ActionListener()
787 public void actionPerformed(ActionEvent e)
789 justifyRightMenuItem_actionPerformed(e);
792 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
793 viewBoxesMenuItem.setState(true);
794 viewBoxesMenuItem.addActionListener(new ActionListener()
797 public void actionPerformed(ActionEvent e)
799 viewBoxesMenuItem_actionPerformed(e);
802 viewTextMenuItem.setText(MessageManager.getString("action.text"));
803 viewTextMenuItem.setState(true);
804 viewTextMenuItem.addActionListener(new ActionListener()
807 public void actionPerformed(ActionEvent e)
809 viewTextMenuItem_actionPerformed(e);
812 showNonconservedMenuItem.setText(MessageManager
813 .getString("label.show_non_conversed"));
814 showNonconservedMenuItem.setState(false);
815 showNonconservedMenuItem.addActionListener(new ActionListener()
818 public void actionPerformed(ActionEvent e)
820 showUnconservedMenuItem_actionPerformed(e);
823 sortPairwiseMenuItem.setText(MessageManager
824 .getString("action.by_pairwise_id"));
825 sortPairwiseMenuItem.addActionListener(new ActionListener()
828 public void actionPerformed(ActionEvent e)
830 sortPairwiseMenuItem_actionPerformed(e);
833 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
834 sortIDMenuItem.addActionListener(new ActionListener()
837 public void actionPerformed(ActionEvent e)
839 sortIDMenuItem_actionPerformed(e);
843 .setText(MessageManager.getString("action.by_length"));
844 sortLengthMenuItem.addActionListener(new ActionListener()
847 public void actionPerformed(ActionEvent e)
849 sortLengthMenuItem_actionPerformed(e);
852 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
853 sortGroupMenuItem.addActionListener(new ActionListener()
856 public void actionPerformed(ActionEvent e)
858 sortGroupMenuItem_actionPerformed(e);
862 removeRedundancyMenuItem.setText(MessageManager.getString(
863 "action.remove_redundancy").concat("..."));
864 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
865 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
866 al = new ActionListener()
869 public void actionPerformed(ActionEvent e)
871 removeRedundancyMenuItem_actionPerformed(e);
874 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
876 pairwiseAlignmentMenuItem.setText(MessageManager
877 .getString("action.pairwise_alignment"));
878 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
881 public void actionPerformed(ActionEvent e)
883 pairwiseAlignmentMenuItem_actionPerformed(e);
886 PCAMenuItem.setText(MessageManager
887 .getString("label.principal_component_analysis"));
888 PCAMenuItem.addActionListener(new ActionListener()
891 public void actionPerformed(ActionEvent e)
893 PCAMenuItem_actionPerformed(e);
896 averageDistanceTreeMenuItem.setText(MessageManager
897 .getString("label.average_distance_identity"));
898 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
901 public void actionPerformed(ActionEvent e)
903 averageDistanceTreeMenuItem_actionPerformed(e);
906 neighbourTreeMenuItem.setText(MessageManager
907 .getString("label.neighbour_joining_identity"));
908 neighbourTreeMenuItem.addActionListener(new ActionListener()
911 public void actionPerformed(ActionEvent e)
913 neighbourTreeMenuItem_actionPerformed(e);
916 this.getContentPane().setLayout(borderLayout1);
917 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
918 statusBar.setBackground(Color.white);
919 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
920 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
921 statusBar.setText(MessageManager.getString("label.status_bar"));
922 outputTextboxMenu.setText(MessageManager
923 .getString("label.out_to_textbox"));
924 clustalColour.setText(MessageManager.getString("label.clustalx"));
926 clustalColour.addActionListener(new ActionListener()
929 public void actionPerformed(ActionEvent e)
931 clustalColour_actionPerformed(e);
934 zappoColour.setText(MessageManager.getString("label.zappo"));
935 zappoColour.addActionListener(new ActionListener()
938 public void actionPerformed(ActionEvent e)
940 zappoColour_actionPerformed(e);
943 taylorColour.setText(MessageManager.getString("label.taylor"));
944 taylorColour.addActionListener(new ActionListener()
947 public void actionPerformed(ActionEvent e)
949 taylorColour_actionPerformed(e);
952 hydrophobicityColour.setText(MessageManager
953 .getString("label.hydrophobicity"));
954 hydrophobicityColour.addActionListener(new ActionListener()
957 public void actionPerformed(ActionEvent e)
959 hydrophobicityColour_actionPerformed(e);
962 helixColour.setText(MessageManager.getString("label.helix_propensity"));
963 helixColour.addActionListener(new ActionListener()
966 public void actionPerformed(ActionEvent e)
968 helixColour_actionPerformed(e);
971 strandColour.setText(MessageManager
972 .getString("label.strand_propensity"));
973 strandColour.addActionListener(new ActionListener()
976 public void actionPerformed(ActionEvent e)
978 strandColour_actionPerformed(e);
981 turnColour.setText(MessageManager.getString("label.turn_propensity"));
982 turnColour.addActionListener(new ActionListener()
985 public void actionPerformed(ActionEvent e)
987 turnColour_actionPerformed(e);
990 buriedColour.setText(MessageManager.getString("label.buried_index"));
991 buriedColour.addActionListener(new ActionListener()
994 public void actionPerformed(ActionEvent e)
996 buriedColour_actionPerformed(e);
999 userDefinedColour.setText(MessageManager
1000 .getString("action.user_defined"));
1001 userDefinedColour.addActionListener(new ActionListener()
1004 public void actionPerformed(ActionEvent e)
1006 userDefinedColour_actionPerformed(e);
1010 .setText(MessageManager.getString("label.percentage_identity"));
1011 PIDColour.addActionListener(new ActionListener()
1014 public void actionPerformed(ActionEvent e)
1016 PIDColour_actionPerformed(e);
1020 .setText(MessageManager.getString("label.blosum62_score"));
1021 BLOSUM62Colour.addActionListener(new ActionListener()
1024 public void actionPerformed(ActionEvent e)
1026 BLOSUM62Colour_actionPerformed(e);
1029 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1030 nucleotideColour.addActionListener(new ActionListener()
1033 public void actionPerformed(ActionEvent e)
1035 nucleotideColour_actionPerformed(e);
1039 purinePyrimidineColour.setText(MessageManager
1040 .getString("label.purine_pyrimidine"));
1041 purinePyrimidineColour.addActionListener(new ActionListener()
1044 public void actionPerformed(ActionEvent e)
1046 purinePyrimidineColour_actionPerformed(e);
1050 RNAInteractionColour.setText("RNA Interaction type");
1051 RNAInteractionColour.addActionListener(new ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 RNAInteractionColour_actionPerformed(e);
1060 * covariationColour.setText("Covariation");
1061 * covariationColour.addActionListener(new ActionListener() { public void
1062 * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
1066 avDistanceTreeBlosumMenuItem.setText(MessageManager
1067 .getString("label.average_distance_bloslum62"));
1068 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
1071 public void actionPerformed(ActionEvent e)
1073 avTreeBlosumMenuItem_actionPerformed(e);
1076 njTreeBlosumMenuItem.setText(MessageManager
1077 .getString("label.neighbour_blosum62"));
1078 njTreeBlosumMenuItem.addActionListener(new ActionListener()
1081 public void actionPerformed(ActionEvent e)
1083 njTreeBlosumMenuItem_actionPerformed(e);
1086 annotationPanelMenuItem.setActionCommand("");
1087 annotationPanelMenuItem.setText(MessageManager
1088 .getString("label.show_annotations"));
1089 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1091 annotationPanelMenuItem.addActionListener(new ActionListener()
1094 public void actionPerformed(ActionEvent e)
1096 annotationPanelMenuItem_actionPerformed(e);
1099 showAllAlAnnotations.setText(MessageManager
1100 .getString("label.show_all_al_annotations"));
1101 final boolean isAnnotationPanelShown = annotationPanelMenuItem
1103 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1104 showAllAlAnnotations.addActionListener(new ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 showAllAnnotations_actionPerformed(false, true);
1112 hideAllAlAnnotations.setText(MessageManager
1113 .getString("label.hide_all_al_annotations"));
1114 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1115 hideAllAlAnnotations.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 hideAllAnnotations_actionPerformed(false, true);
1123 showAllSeqAnnotations.setText(MessageManager
1124 .getString("label.show_all_seq_annotations"));
1125 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1126 showAllSeqAnnotations.addActionListener(new ActionListener()
1129 public void actionPerformed(ActionEvent e)
1131 showAllAnnotations_actionPerformed(true, false);
1134 hideAllSeqAnnotations.setText(MessageManager
1135 .getString("label.hide_all_seq_annotations"));
1136 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1137 hideAllSeqAnnotations.addActionListener(new ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 hideAllAnnotations_actionPerformed(true, false);
1145 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1146 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
1147 SequenceAnnotationOrder.NONE.name()));
1148 sortAnnBySequence.setText(MessageManager
1149 .getString("label.sort_annotations_by_sequence"));
1151 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1152 sortAnnBySequence.addActionListener(new ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 boolean newState = sortAnnBySequence.getState();
1158 sortAnnByLabel.setSelected(false);
1159 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1160 : SequenceAnnotationOrder.NONE);
1161 sortAnnotations_actionPerformed();
1164 sortAnnByLabel.setText(MessageManager
1165 .getString("label.sort_annotations_by_label"));
1167 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1168 sortAnnByLabel.addActionListener(new ActionListener()
1171 public void actionPerformed(ActionEvent e)
1173 boolean newState = sortAnnByLabel.getState();
1174 sortAnnBySequence.setSelected(false);
1175 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1176 : SequenceAnnotationOrder.NONE);
1177 sortAnnotations_actionPerformed();
1180 colourTextMenuItem.setText(MessageManager
1181 .getString("label.colour_text"));
1182 colourTextMenuItem.addActionListener(new ActionListener()
1185 public void actionPerformed(ActionEvent e)
1187 colourTextMenuItem_actionPerformed(e);
1190 htmlMenuItem.setText(MessageManager.getString("label.html"));
1191 htmlMenuItem.addActionListener(new ActionListener()
1194 public void actionPerformed(ActionEvent e)
1196 htmlMenuItem_actionPerformed(e);
1199 overviewMenuItem.setText(MessageManager
1200 .getString("label.overview_window"));
1201 overviewMenuItem.addActionListener(new ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 overviewMenuItem_actionPerformed(e);
1210 undoMenuItem.setEnabled(false);
1211 undoMenuItem.setText(MessageManager.getString("action.undo"));
1212 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
1213 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1214 al = new ActionListener()
1217 public void actionPerformed(ActionEvent e)
1219 undoMenuItem_actionPerformed(e);
1222 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
1224 redoMenuItem.setEnabled(false);
1225 redoMenuItem.setText(MessageManager.getString("action.redo"));
1226 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
1227 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1228 al = new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 redoMenuItem_actionPerformed(e);
1236 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
1238 conservationMenuItem.setText(MessageManager
1239 .getString("action.by_conservation"));
1240 conservationMenuItem.addActionListener(new ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 conservationMenuItem_actionPerformed(e);
1248 noColourmenuItem.setText(MessageManager.getString("label.none"));
1249 noColourmenuItem.addActionListener(new ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 noColourmenuItem_actionPerformed(e);
1257 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1258 wrapMenuItem.addActionListener(new ActionListener()
1261 public void actionPerformed(ActionEvent e)
1263 wrapMenuItem_actionPerformed(e);
1267 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1268 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
1269 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1270 al = new ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 printMenuItem_actionPerformed(e);
1278 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
1281 .setText(MessageManager.getString("action.show_gaps"));
1282 renderGapsMenuItem.setState(true);
1283 renderGapsMenuItem.addActionListener(new ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 renderGapsMenuItem_actionPerformed(e);
1292 findMenuItem.setText(MessageManager.getString("action.find"));
1293 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
1294 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1295 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1296 MessageManager.getString("label.find_tip")));
1297 al = new ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 findMenuItem_actionPerformed(e);
1305 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
1307 abovePIDThreshold.setText(MessageManager
1308 .getString("label.above_identity_threshold"));
1309 abovePIDThreshold.addActionListener(new ActionListener()
1312 public void actionPerformed(ActionEvent e)
1314 abovePIDThreshold_actionPerformed(e);
1317 showSeqFeatures.setText(MessageManager
1318 .getString("label.show_sequence_features"));
1319 showSeqFeatures.addActionListener(new ActionListener()
1322 public void actionPerformed(ActionEvent actionEvent)
1324 showSeqFeatures_actionPerformed(actionEvent);
1328 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1329 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1330 * void actionPerformed(ActionEvent actionEvent) {
1331 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1333 showDbRefsMenuitem.setText(MessageManager
1334 .getString("label.show_database_refs"));
1335 showDbRefsMenuitem.addActionListener(new ActionListener()
1339 public void actionPerformed(ActionEvent e)
1341 showDbRefs_actionPerformed(e);
1345 showNpFeatsMenuitem.setText(MessageManager
1346 .getString("label.show_non_positional_features"));
1347 showNpFeatsMenuitem.addActionListener(new ActionListener()
1351 public void actionPerformed(ActionEvent e)
1353 showNpFeats_actionPerformed(e);
1357 showGroupConservation.setText(MessageManager
1358 .getString("label.group_conservation"));
1359 showGroupConservation.addActionListener(new ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 showGroupConservation_actionPerformed(e);
1370 showGroupConsensus.setText(MessageManager
1371 .getString("label.group_consensus"));
1372 showGroupConsensus.addActionListener(new ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 showGroupConsensus_actionPerformed(e);
1382 showConsensusHistogram.setText(MessageManager
1383 .getString("label.show_consensus_histogram"));
1384 showConsensusHistogram.addActionListener(new ActionListener()
1388 public void actionPerformed(ActionEvent e)
1390 showConsensusHistogram_actionPerformed(e);
1394 showSequenceLogo.setText(MessageManager
1395 .getString("label.show_consensus_logo"));
1396 showSequenceLogo.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 showSequenceLogo_actionPerformed(e);
1406 normaliseSequenceLogo.setText(MessageManager
1407 .getString("label.norm_consensus_logo"));
1408 normaliseSequenceLogo.addActionListener(new ActionListener()
1412 public void actionPerformed(ActionEvent e)
1414 normaliseSequenceLogo_actionPerformed(e);
1418 applyAutoAnnotationSettings.setText(MessageManager
1419 .getString("label.apply_all_groups"));
1420 applyAutoAnnotationSettings.setState(false);
1421 applyAutoAnnotationSettings.setVisible(true);
1422 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 applyAutoAnnotationSettings_actionPerformed(e);
1431 ButtonGroup buttonGroup = new ButtonGroup();
1432 buttonGroup.add(showAutoFirst);
1433 buttonGroup.add(showAutoLast);
1434 showAutoFirst.setText(MessageManager.getString("label.show_first"));
1435 showAutoFirst.setSelected(Cache.getDefault(
1436 Preferences.SHOW_AUTOCALC_ABOVE, false));
1437 showAutoFirst.addActionListener(new ActionListener()
1440 public void actionPerformed(ActionEvent e)
1442 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1443 sortAnnotations_actionPerformed();
1446 showAutoLast.setText(MessageManager.getString("label.show_last"));
1447 showAutoLast.setSelected(!showAutoFirst.isSelected());
1448 showAutoLast.addActionListener(new ActionListener()
1451 public void actionPerformed(ActionEvent e)
1453 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1454 sortAnnotations_actionPerformed();
1458 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1459 nucleotideColour.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 nucleotideColour_actionPerformed(e);
1468 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1469 tcoffeeColour.setEnabled(false);
1470 tcoffeeColour.addActionListener(new ActionListener()
1474 public void actionPerformed(ActionEvent e)
1476 tcoffeeColorScheme_actionPerformed(e);
1481 .setText(MessageManager.getString("action.undefine_groups"));
1482 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1483 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1484 al = new ActionListener()
1487 public void actionPerformed(ActionEvent e)
1489 deleteGroups_actionPerformed(e);
1492 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1494 createGroup.setText(MessageManager.getString("action.create_groups"));
1495 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1496 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1497 al = new ActionListener()
1500 public void actionPerformed(ActionEvent e)
1502 createGroup_actionPerformed(e);
1505 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1507 unGroup.setText(MessageManager.getString("action.remove_group"));
1508 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1509 .getDefaultToolkit().getMenuShortcutKeyMask()
1510 | KeyEvent.SHIFT_MASK, false);
1511 al = new ActionListener()
1514 public void actionPerformed(ActionEvent e)
1516 unGroup_actionPerformed(e);
1519 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1521 copy.setText(MessageManager.getString("action.copy"));
1522 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1523 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1525 al = new ActionListener()
1528 public void actionPerformed(ActionEvent e)
1530 copy_actionPerformed(e);
1533 addMenuActionAndAccelerator(keyStroke, copy, al);
1535 cut.setText(MessageManager.getString("action.cut"));
1536 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1537 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1538 al = new ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 cut_actionPerformed(e);
1546 addMenuActionAndAccelerator(keyStroke, cut, al);
1548 delete.setText(MessageManager.getString("action.delete"));
1549 delete.addActionListener(new ActionListener()
1552 public void actionPerformed(ActionEvent e)
1554 delete_actionPerformed(e);
1558 pasteMenu.setText(MessageManager.getString("action.paste"));
1559 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1560 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1561 .getDefaultToolkit().getMenuShortcutKeyMask()
1562 | KeyEvent.SHIFT_MASK, false);
1563 al = new ActionListener()
1566 public void actionPerformed(ActionEvent e)
1568 pasteNew_actionPerformed(e);
1571 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1573 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1574 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1575 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1576 al = new ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 pasteThis_actionPerformed(e);
1584 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1586 applyToAllGroups.setText(MessageManager
1587 .getString("label.apply_colour_to_all_groups"));
1588 applyToAllGroups.addActionListener(new ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 applyToAllGroups_actionPerformed(e);
1596 createPNG.addActionListener(new ActionListener()
1599 public void actionPerformed(ActionEvent e)
1604 createPNG.setActionCommand(MessageManager
1605 .getString("label.save_png_image"));
1606 createPNG.setText("PNG");
1608 font.setText(MessageManager.getString("action.font"));
1609 font.addActionListener(new ActionListener()
1612 public void actionPerformed(ActionEvent e)
1614 font_actionPerformed(e);
1618 seqLimits.setText(MessageManager
1619 .getString("label.show_sequence_limits"));
1620 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1621 seqLimits.addActionListener(new ActionListener()
1624 public void actionPerformed(ActionEvent e)
1626 seqLimit_actionPerformed(e);
1629 epsFile.setText("EPS");
1630 epsFile.addActionListener(new ActionListener()
1633 public void actionPerformed(ActionEvent e)
1639 createSVG.setText("SVG");
1640 createSVG.addActionListener(new ActionListener()
1643 public void actionPerformed(ActionEvent e)
1649 LoadtreeMenuItem.setActionCommand(MessageManager
1650 .getString("label.load_tree_for_sequence_set"));
1651 LoadtreeMenuItem.setText(MessageManager
1652 .getString("label.load_associated_tree"));
1653 LoadtreeMenuItem.addActionListener(new ActionListener()
1656 public void actionPerformed(ActionEvent e)
1658 LoadtreeMenuItem_actionPerformed(e);
1662 scaleAbove.setVisible(false);
1663 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1664 scaleAbove.addActionListener(new ActionListener()
1667 public void actionPerformed(ActionEvent e)
1669 scaleAbove_actionPerformed(e);
1672 scaleLeft.setVisible(false);
1673 scaleLeft.setSelected(true);
1674 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1675 scaleLeft.addActionListener(new ActionListener()
1678 public void actionPerformed(ActionEvent e)
1680 scaleLeft_actionPerformed(e);
1683 scaleRight.setVisible(false);
1684 scaleRight.setSelected(true);
1685 scaleRight.setText(MessageManager.getString("action.scale_right"));
1686 scaleRight.addActionListener(new ActionListener()
1689 public void actionPerformed(ActionEvent e)
1691 scaleRight_actionPerformed(e);
1694 centreColumnLabelsMenuItem.setVisible(true);
1695 centreColumnLabelsMenuItem.setState(false);
1696 centreColumnLabelsMenuItem.setText(MessageManager
1697 .getString("label.centre_column_labels"));
1698 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1701 public void actionPerformed(ActionEvent e)
1703 centreColumnLabels_actionPerformed(e);
1706 followHighlightMenuItem.setVisible(true);
1707 followHighlightMenuItem.setState(true);
1708 followHighlightMenuItem.setText(MessageManager
1709 .getString("label.automatic_scrolling"));
1710 followHighlightMenuItem.addActionListener(new ActionListener()
1714 public void actionPerformed(ActionEvent e)
1716 followHighlight_actionPerformed();
1721 modifyPID.setText(MessageManager
1722 .getString("label.modify_identity_thereshold"));
1723 modifyPID.addActionListener(new ActionListener()
1726 public void actionPerformed(ActionEvent e)
1728 modifyPID_actionPerformed(e);
1731 modifyConservation.setText(MessageManager
1732 .getString("label.modify_conservation_thereshold"));
1733 modifyConservation.addActionListener(new ActionListener()
1736 public void actionPerformed(ActionEvent e)
1738 modifyConservation_actionPerformed(e);
1742 .setText(MessageManager.getString("action.by_tree_order"));
1743 sort.setText(MessageManager.getString("action.sort"));
1744 sort.addMenuListener(new MenuListener()
1747 public void menuSelected(MenuEvent e)
1753 public void menuDeselected(MenuEvent e)
1758 public void menuCanceled(MenuEvent e)
1762 sortByAnnotScore.setText(MessageManager
1763 .getString("label.sort_by_score"));
1764 sort.add(sortByAnnotScore);
1765 sort.addMenuListener(new javax.swing.event.MenuListener()
1769 public void menuCanceled(MenuEvent e)
1774 public void menuDeselected(MenuEvent e)
1779 public void menuSelected(MenuEvent e)
1781 buildSortByAnnotationScoresMenu();
1784 sortByAnnotScore.setVisible(false);
1787 .setText(MessageManager.getString("action.calculate_tree"));
1789 jMenu2.setText(MessageManager.getString("label.export_image"));
1790 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1791 padGapsMenuitem.setState(jalview.bin.Cache
1792 .getDefault("PAD_GAPS", false));
1793 padGapsMenuitem.addActionListener(new ActionListener()
1796 public void actionPerformed(ActionEvent e)
1798 padGapsMenuitem_actionPerformed(e);
1801 vamsasStore.setVisible(false);
1802 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1803 vamsasStore.addActionListener(new ActionListener()
1806 public void actionPerformed(ActionEvent e)
1808 vamsasStore_actionPerformed(e);
1811 showTranslation.setText(MessageManager
1812 .getString("label.translate_cDNA"));
1813 showTranslation.addActionListener(new ActionListener()
1816 public void actionPerformed(ActionEvent e)
1818 showTranslation_actionPerformed(e);
1825 cdna.setText(MessageManager.getString("label.cdna"));
1826 // link to available cDNA
1827 JMenuItem linkCdna = new JMenuItem(
1828 MessageManager.getString("label.link_cdna"));
1829 linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1830 MessageManager.getString("label.link_cdna_tip")));
1831 linkCdna.addActionListener(new ActionListener()
1834 public void actionPerformed(ActionEvent e)
1836 linkCdna_actionPerformed();
1840 // align linked cDNA
1841 JMenuItem alignCdna = new JMenuItem(
1842 MessageManager.getString("label.align_cdna"));
1843 alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1844 MessageManager.getString("label.align_cdna_tip")));
1845 alignCdna.addActionListener(new ActionListener()
1848 public void actionPerformed(ActionEvent e)
1850 alignCdna_actionPerformed();
1853 cdna.add(alignCdna);
1855 // view alignment as cDNA (when known)
1856 JMenuItem viewAsCdna = new JMenuItem(
1857 MessageManager.getString("label.view_as_cdna"));
1858 viewAsCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1859 MessageManager.getString("label.view_as_cdna_tip")));
1860 viewAsCdna.addActionListener(new ActionListener()
1863 public void actionPerformed(ActionEvent e)
1865 viewAsCdna_actionPerformed();
1868 cdna.add(viewAsCdna);
1870 extractScores.setText(MessageManager.getString("label.extract_scores")
1872 extractScores.addActionListener(new ActionListener()
1875 public void actionPerformed(ActionEvent e)
1877 extractScores_actionPerformed(e);
1880 extractScores.setVisible(true);
1881 // JBPNote: TODO: make gui for regex based score extraction
1883 // for show products actions see AlignFrame.canShowProducts
1884 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1885 openFeatureSettings.setText(MessageManager
1886 .getString("label.feature_settings"));
1887 openFeatureSettings.addActionListener(new ActionListener()
1890 public void actionPerformed(ActionEvent e)
1892 featureSettings_actionPerformed(e);
1896 .setText(MessageManager.getString("label.fetch_sequences"));
1897 fetchSequence.addActionListener(new ActionListener()
1900 public void actionPerformed(ActionEvent e)
1902 fetchSequence_actionPerformed(e);
1906 annotationColour.setText(MessageManager
1907 .getString("action.by_annotation"));
1908 annotationColour.addActionListener(new ActionListener()
1911 public void actionPerformed(ActionEvent e)
1913 annotationColour_actionPerformed(e);
1917 rnahelicesColour.setText(MessageManager
1918 .getString("action.by_rna_helixes"));
1919 rnahelicesColour.addActionListener(new ActionListener()
1922 public void actionPerformed(ActionEvent e)
1924 rnahelicesColour_actionPerformed(e);
1928 associatedData.setText(MessageManager
1929 .getString("label.load_features_annotations"));
1930 associatedData.addActionListener(new ActionListener()
1933 public void actionPerformed(ActionEvent e)
1935 associatedData_actionPerformed(e);
1938 autoCalculate.setText(MessageManager
1939 .getString("label.autocalculate_consensus"));
1940 autoCalculate.setState(jalview.bin.Cache.getDefault(
1941 "AUTO_CALC_CONSENSUS", true));
1942 autoCalculate.addActionListener(new ActionListener()
1945 public void actionPerformed(ActionEvent e)
1947 autoCalculate_actionPerformed(e);
1950 sortByTree.setText(MessageManager
1951 .getString("label.sort_alignment_new_tree"));
1953 .setToolTipText("<html>"
1955 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1957 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1958 sortByTree.addActionListener(new ActionListener()
1961 public void actionPerformed(ActionEvent e)
1963 sortByTreeOption_actionPerformed(e);
1967 listenToViewSelections.setText(MessageManager
1968 .getString("label.listen_for_selections"));
1969 listenToViewSelections
1970 .setToolTipText("<html>"
1972 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1973 listenToViewSelections.setState(false);
1974 listenToViewSelections.addActionListener(new ActionListener()
1977 public void actionPerformed(ActionEvent e)
1979 listenToViewSelections_actionPerformed(e);
1984 .setText(MessageManager.getString("label.add_sequences"));
1985 addFromFile.setText(MessageManager.getString("label.from_file"));
1986 addFromFile.addActionListener(new ActionListener()
1989 public void actionPerformed(ActionEvent e)
1991 addFromFile_actionPerformed(e);
1994 addFromText.setText(MessageManager.getString("label.from_textbox"));
1995 addFromText.addActionListener(new ActionListener()
1998 public void actionPerformed(ActionEvent e)
2000 addFromText_actionPerformed(e);
2003 addFromURL.setText(MessageManager.getString("label.from_url"));
2004 addFromURL.addActionListener(new ActionListener()
2007 public void actionPerformed(ActionEvent e)
2009 addFromURL_actionPerformed(e);
2012 exportFeatures.setText(MessageManager
2013 .getString("label.export_features"));
2014 exportFeatures.addActionListener(new ActionListener()
2017 public void actionPerformed(ActionEvent e)
2019 exportFeatures_actionPerformed(e);
2022 exportAnnotations.setText(MessageManager
2023 .getString("label.export_annotations"));
2024 exportAnnotations.addActionListener(new ActionListener()
2027 public void actionPerformed(ActionEvent e)
2029 exportAnnotations_actionPerformed(e);
2032 statusPanel.setLayout(gridLayout1);
2033 jMenu3.setText(MessageManager.getString("action.show"));
2034 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
2035 showAllSeqs.setToolTipText(MessageManager
2036 .getString("label.toggle_sequence_visibility"));
2037 showAllSeqs.addActionListener(new ActionListener()
2040 public void actionPerformed(ActionEvent e)
2042 showAllSeqs_actionPerformed(e);
2045 showAllColumns.setText(MessageManager.getString("label.all_columns"));
2046 showAllColumns.setToolTipText(MessageManager
2047 .getString("label.toggle_columns_visibility"));
2048 showAllColumns.addActionListener(new ActionListener()
2051 public void actionPerformed(ActionEvent e)
2053 showAllColumns_actionPerformed(e);
2056 hideMenu.setText(MessageManager.getString("action.hide"));
2057 hideSelSequences.setText(MessageManager
2058 .getString("label.selected_sequences"));
2059 hideSelSequences.setToolTipText(MessageManager
2060 .getString("label.toggle_sequence_visibility"));
2061 hideSelSequences.addActionListener(new ActionListener()
2064 public void actionPerformed(ActionEvent e)
2066 hideSelSequences_actionPerformed(e);
2069 hideSelColumns.setText(MessageManager
2070 .getString("label.selected_columns"));
2071 hideSelColumns.setToolTipText(MessageManager
2072 .getString("label.toggle_columns_visibility"));
2073 hideSelColumns.addActionListener(new ActionListener()
2076 public void actionPerformed(ActionEvent e)
2078 hideSelColumns_actionPerformed(e);
2081 hideAllSelection.setText(MessageManager
2082 .getString("label.selected_region"));
2083 hideAllSelection.addActionListener(new ActionListener()
2086 public void actionPerformed(ActionEvent e)
2088 hideAllSelection_actionPerformed(e);
2091 // TODO: should be hidden if no selection exists.
2092 hideAllButSelection.setText(MessageManager
2093 .getString("label.all_but_selected_region"));
2094 hideAllButSelection.addActionListener(new ActionListener()
2097 public void actionPerformed(ActionEvent e)
2099 hideAllButSelection_actionPerformed(e);
2102 showAllhidden.setText(MessageManager
2103 .getString("label.all_sequences_columns"));
2104 showAllhidden.setToolTipText(MessageManager
2105 .getString("label.toggles_visibility_hidden_selected_regions"));
2106 showAllhidden.addActionListener(new ActionListener()
2109 public void actionPerformed(ActionEvent e)
2111 showAllhidden_actionPerformed(e);
2114 hiddenMarkers.setText(MessageManager
2115 .getString("action.show_hidden_markers"));
2116 hiddenMarkers.addActionListener(new ActionListener()
2119 public void actionPerformed(ActionEvent e)
2121 hiddenMarkers_actionPerformed(e);
2125 invertColSel.setText(MessageManager
2126 .getString("action.invert_column_selection"));
2127 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
2128 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
2129 | KeyEvent.ALT_MASK, false);
2130 al = new ActionListener()
2133 public void actionPerformed(ActionEvent e)
2135 invertColSel_actionPerformed(e);
2138 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
2140 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2143 public void stateChanged(ChangeEvent evt)
2145 JTabbedPane pane = (JTabbedPane) evt.getSource();
2146 int sel = pane.getSelectedIndex();
2147 tabSelectionChanged(sel);
2150 tabbedPane.addMouseListener(new MouseAdapter()
2153 public void mousePressed(MouseEvent e)
2155 tabbedPane_mousePressed(e);
2158 tabbedPane.addFocusListener(new FocusAdapter()
2161 public void focusGained(FocusEvent e)
2163 tabbedPane_focusGained(e);
2167 save.setText(MessageManager.getString("action.save"));
2168 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
2169 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2170 al = new ActionListener()
2173 public void actionPerformed(ActionEvent e)
2175 save_actionPerformed(e);
2178 addMenuActionAndAccelerator(keyStroke, save, al);
2180 reload.setEnabled(false);
2181 reload.setText(MessageManager.getString("action.reload"));
2182 reload.addActionListener(new ActionListener()
2185 public void actionPerformed(ActionEvent e)
2187 reload_actionPerformed(e);
2191 newView.setText(MessageManager.getString("action.new_view"));
2192 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
2193 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2194 al = new ActionListener()
2197 public void actionPerformed(ActionEvent e)
2199 newView_actionPerformed(e);
2202 addMenuActionAndAccelerator(keyStroke, newView, al);
2204 tabbedPane.setToolTipText("<html><i>"
2205 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2207 textColour.setText(MessageManager.getString("label.colour_text")
2209 textColour.addActionListener(new ActionListener()
2212 public void actionPerformed(ActionEvent e)
2214 textColour_actionPerformed(e);
2217 formatMenu.setText(MessageManager.getString("action.format"));
2218 selectMenu.setText(MessageManager.getString("action.select"));
2219 idRightAlign.setText(MessageManager
2220 .getString("label.right_align_sequence_id"));
2221 idRightAlign.addActionListener(new ActionListener()
2224 public void actionPerformed(ActionEvent e)
2226 idRightAlign_actionPerformed(e);
2230 gatherViews.setEnabled(false);
2231 gatherViews.setText(MessageManager.getString("action.gather_views"));
2232 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
2233 al = new ActionListener()
2236 public void actionPerformed(ActionEvent e)
2238 gatherViews_actionPerformed(e);
2241 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
2243 expandViews.setEnabled(false);
2244 expandViews.setText(MessageManager.getString("action.expand_views"));
2245 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
2246 al = new ActionListener()
2249 public void actionPerformed(ActionEvent e)
2251 expandViews_actionPerformed(e);
2254 addMenuActionAndAccelerator(keyStroke, expandViews, al);
2257 .setText(MessageManager.getString("action.page_setup") + "...");
2258 pageSetup.addActionListener(new ActionListener()
2261 public void actionPerformed(ActionEvent e)
2263 pageSetup_actionPerformed(e);
2266 alignmentProperties.setText(MessageManager
2267 .getString("label.alignment_props") + "...");
2268 alignmentProperties.addActionListener(new ActionListener()
2271 public void actionPerformed(ActionEvent actionEvent)
2273 alignmentProperties();
2276 tooltipSettingsMenu.setText(MessageManager
2277 .getString("label.sequence_id_tooltip"));
2278 autoAnnMenu.setText(MessageManager
2279 .getString("label.autocalculated_annotation"));
2280 alignFrameMenuBar.add(fileMenu);
2281 alignFrameMenuBar.add(editMenu);
2282 alignFrameMenuBar.add(selectMenu);
2283 alignFrameMenuBar.add(viewMenu);
2284 alignFrameMenuBar.add(annotationsMenu);
2285 alignFrameMenuBar.add(formatMenu);
2286 alignFrameMenuBar.add(colourMenu);
2287 alignFrameMenuBar.add(calculateMenu);
2288 alignFrameMenuBar.add(webService);
2289 fileMenu.add(fetchSequence);
2290 fileMenu.add(addSequenceMenu);
2291 fileMenu.add(reload);
2292 fileMenu.addSeparator();
2293 fileMenu.add(vamsasStore);
2295 fileMenu.add(saveAs);
2296 fileMenu.add(outputTextboxMenu);
2297 fileMenu.add(pageSetup);
2298 fileMenu.add(printMenuItem);
2299 fileMenu.addSeparator();
2300 fileMenu.add(jMenu2);
2301 fileMenu.add(exportFeatures);
2302 fileMenu.add(exportAnnotations);
2303 fileMenu.add(LoadtreeMenuItem);
2304 fileMenu.add(associatedData);
2305 fileMenu.addSeparator();
2306 fileMenu.add(closeMenuItem);
2307 editMenu.add(undoMenuItem);
2308 editMenu.add(redoMenuItem);
2311 editMenu.add(pasteMenu);
2312 editMenu.add(delete);
2313 editMenu.addSeparator();
2314 editMenu.add(remove2LeftMenuItem);
2315 editMenu.add(remove2RightMenuItem);
2316 editMenu.add(removeGappedColumnMenuItem);
2317 editMenu.add(removeAllGapsMenuItem);
2318 editMenu.add(removeRedundancyMenuItem);
2319 editMenu.addSeparator();
2320 // dont add these yet in the CVS build - they cannot be undone!
2321 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2322 // editMenu.add(justifyLeftMenuItem);
2323 // editMenu.add(justifyRightMenuItem);
2324 // editMenu.addSeparator();
2325 editMenu.add(padGapsMenuitem);
2326 viewMenu.add(newView);
2327 viewMenu.add(expandViews);
2328 viewMenu.add(gatherViews);
2329 viewMenu.addSeparator();
2330 viewMenu.add(jMenu3);
2331 viewMenu.add(hideMenu);
2332 viewMenu.addSeparator();
2333 viewMenu.add(followHighlightMenuItem);
2334 annotationsMenu.add(annotationPanelMenuItem);
2335 annotationsMenu.addSeparator();
2336 annotationsMenu.add(showAllAlAnnotations);
2337 annotationsMenu.add(hideAllAlAnnotations);
2338 annotationsMenu.addSeparator();
2339 annotationsMenu.add(showAllSeqAnnotations);
2340 annotationsMenu.add(hideAllSeqAnnotations);
2341 annotationsMenu.add(sortAnnBySequence);
2342 annotationsMenu.add(sortAnnByLabel);
2343 annotationsMenu.addSeparator();
2344 autoAnnMenu.add(showAutoFirst);
2345 autoAnnMenu.add(showAutoLast);
2346 autoAnnMenu.addSeparator();
2347 autoAnnMenu.add(applyAutoAnnotationSettings);
2348 autoAnnMenu.add(showConsensusHistogram);
2349 autoAnnMenu.add(showSequenceLogo);
2350 autoAnnMenu.add(normaliseSequenceLogo);
2351 autoAnnMenu.addSeparator();
2352 autoAnnMenu.add(showGroupConservation);
2353 autoAnnMenu.add(showGroupConsensus);
2354 annotationsMenu.add(autoAnnMenu);
2355 viewMenu.addSeparator();
2356 viewMenu.add(showSeqFeatures);
2357 // viewMenu.add(showSeqFeaturesHeight);
2359 viewMenu.add(openFeatureSettings);
2360 tooltipSettingsMenu.add(showDbRefsMenuitem);
2361 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2362 viewMenu.add(tooltipSettingsMenu);
2363 viewMenu.addSeparator();
2364 viewMenu.add(alignmentProperties);
2365 viewMenu.addSeparator();
2366 viewMenu.add(overviewMenuItem);
2367 colourMenu.add(applyToAllGroups);
2368 colourMenu.add(textColour);
2369 colourMenu.addSeparator();
2370 colourMenu.add(noColourmenuItem);
2371 colourMenu.add(clustalColour);
2372 colourMenu.add(BLOSUM62Colour);
2373 colourMenu.add(PIDColour);
2374 colourMenu.add(zappoColour);
2375 colourMenu.add(taylorColour);
2376 colourMenu.add(hydrophobicityColour);
2377 colourMenu.add(helixColour);
2378 colourMenu.add(strandColour);
2379 colourMenu.add(turnColour);
2380 colourMenu.add(buriedColour);
2381 colourMenu.add(nucleotideColour);
2382 colourMenu.add(purinePyrimidineColour);
2383 colourMenu.add(RNAInteractionColour);
2384 // colourMenu.add(covariationColour);
2385 colourMenu.add(tcoffeeColour);
2386 colourMenu.add(userDefinedColour);
2387 colourMenu.addSeparator();
2388 colourMenu.add(conservationMenuItem);
2389 colourMenu.add(modifyConservation);
2390 colourMenu.add(abovePIDThreshold);
2391 colourMenu.add(modifyPID);
2392 colourMenu.add(annotationColour);
2393 colourMenu.add(rnahelicesColour);
2394 calculateMenu.add(sort);
2395 calculateMenu.add(calculateTree);
2396 calculateMenu.addSeparator();
2397 calculateMenu.add(pairwiseAlignmentMenuItem);
2398 calculateMenu.add(PCAMenuItem);
2399 calculateMenu.addSeparator();
2400 calculateMenu.add(showTranslation);
2401 calculateMenu.add(cdna);
2402 calculateMenu.add(showProducts);
2403 calculateMenu.add(autoCalculate);
2404 calculateMenu.add(sortByTree);
2405 calculateMenu.addSeparator();
2406 calculateMenu.add(extractScores);
2407 webServiceNoServices = new JMenuItem(
2408 MessageManager.getString("label.no_services"));
2409 webService.add(webServiceNoServices);
2410 pasteMenu.add(pasteNew);
2411 pasteMenu.add(pasteThis);
2412 sort.add(sortIDMenuItem);
2413 sort.add(sortLengthMenuItem);
2414 sort.add(sortGroupMenuItem);
2415 sort.add(sortPairwiseMenuItem);
2416 sort.add(sortByTreeMenu);
2417 jMenu2.add(htmlMenuItem);
2418 jMenu2.add(epsFile);
2419 jMenu2.add(createPNG);
2420 jMenu2.add(createSVG);
2421 addSequenceMenu.add(addFromFile);
2422 addSequenceMenu.add(addFromText);
2423 addSequenceMenu.add(addFromURL);
2424 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2425 statusPanel.add(statusBar, null);
2426 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2427 jMenu3.add(showAllColumns);
2428 jMenu3.add(showAllSeqs);
2429 jMenu3.add(showAllhidden);
2430 hideMenu.add(hideSelColumns);
2431 hideMenu.add(hideSelSequences);
2432 hideMenu.add(hideAllSelection);
2433 hideMenu.add(hideAllButSelection);
2435 formatMenu.add(font);
2436 formatMenu.addSeparator();
2437 formatMenu.add(wrapMenuItem);
2438 formatMenu.add(scaleAbove);
2439 formatMenu.add(scaleLeft);
2440 formatMenu.add(scaleRight);
2441 formatMenu.add(seqLimits);
2442 formatMenu.add(idRightAlign);
2443 formatMenu.add(hiddenMarkers);
2444 formatMenu.add(viewBoxesMenuItem);
2445 formatMenu.add(viewTextMenuItem);
2446 formatMenu.add(colourTextMenuItem);
2447 formatMenu.add(renderGapsMenuItem);
2448 formatMenu.add(centreColumnLabelsMenuItem);
2449 formatMenu.add(showNonconservedMenuItem);
2450 selectMenu.add(findMenuItem);
2451 selectMenu.addSeparator();
2452 selectMenu.add(selectAllSequenceMenuItem);
2453 selectMenu.add(deselectAllSequenceMenuItem);
2454 selectMenu.add(invertSequenceMenuItem);
2455 selectMenu.add(invertColSel);
2456 selectMenu.add(createGroup);
2457 selectMenu.add(unGroup);
2458 selectMenu.add(grpsFromSelection);
2459 selectMenu.add(deleteGroups);
2460 calculateMenu.add(expandAlignment);
2461 // TODO - determine if the listenToViewSelections button is needed : see bug
2463 // selectMenu.addSeparator();
2464 // selectMenu.add(listenToViewSelections);
2468 * Adds the given action listener and key accelerator to the given menu item.
2469 * Also saves in a lookup table to support lookup of action by key stroke.
2473 * @param actionListener
2475 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2476 JMenuItem menuItem, ActionListener actionListener)
2478 menuItem.setAccelerator(keyStroke);
2479 accelerators.put(keyStroke, menuItem);
2480 menuItem.addActionListener(actionListener);
2483 protected void viewAsCdna_actionPerformed()
2487 protected void alignCdna_actionPerformed()
2491 protected void linkCdna_actionPerformed()
2496 * Action on clicking sort annotations by type.
2500 protected void sortAnnotations_actionPerformed()
2505 * Action on clicking Show all annotations.
2507 * @param forSequences
2508 * update sequence-related annotations
2509 * @param forAlignment
2510 * update non-sequence-related annotations
2512 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2513 boolean forAlignment)
2515 setAnnotationsVisibility(true, forSequences, forAlignment);
2519 * Action on clicking Hide all annotations.
2521 * @param forSequences
2522 * update sequence-related annotations
2523 * @param forAlignment
2524 * update non-sequence-related annotations
2526 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2527 boolean forAlignment)
2529 setAnnotationsVisibility(false, forSequences, forAlignment);
2533 * Set the visibility of annotations to true or false. Can act on
2534 * sequence-related annotations, or alignment-related, or both.
2537 * @param forSequences
2538 * update sequence-related annotations
2539 * @param forAlignment
2540 * update non-sequence-related annotations
2542 protected void setAnnotationsVisibility(boolean visible,
2543 boolean forSequences, boolean forAlignment)
2548 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2550 // TODO Auto-generated method stub
2554 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2556 // TODO Auto-generated method stub
2560 protected void showAllhidden_actionPerformed(ActionEvent e)
2562 // TODO Auto-generated method stub
2566 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2568 // TODO Auto-generated method stub
2572 protected void hideAllSelection_actionPerformed(ActionEvent e)
2574 // TODO Auto-generated method stub
2578 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2580 // TODO Auto-generated method stub
2584 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2586 // TODO Auto-generated method stub
2590 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2592 // TODO Auto-generated method stub
2596 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2598 // TODO Auto-generated method stub
2602 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2604 // TODO Auto-generated method stub
2608 protected void showGroupConservation_actionPerformed(ActionEvent e)
2610 // TODO Auto-generated method stub
2614 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2616 // TODO Auto-generated method stub
2620 protected void showSeqFeaturesHeight_actionPerformed(
2621 ActionEvent actionEvent)
2623 // TODO Auto-generated method stub
2627 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2629 // TODO Auto-generated method stub
2633 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2635 // TODO Auto-generated method stub
2639 protected void followHighlight_actionPerformed()
2641 // TODO Auto-generated method stub
2645 protected void showNpFeats_actionPerformed(ActionEvent e)
2647 // TODO Auto-generated method stub
2651 protected void showDbRefs_actionPerformed(ActionEvent e)
2653 // TODO Auto-generated method stub
2657 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2661 protected void buildSortByAnnotationScoresMenu()
2665 protected void extractScores_actionPerformed(ActionEvent e)
2669 protected void outputText_actionPerformed(ActionEvent e)
2673 public void addFromFile_actionPerformed(ActionEvent e)
2678 public void addFromText_actionPerformed(ActionEvent e)
2683 public void addFromURL_actionPerformed(ActionEvent e)
2688 public void exportFeatures_actionPerformed(ActionEvent e)
2693 public void exportAnnotations_actionPerformed(ActionEvent e)
2698 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2702 protected void closeMenuItem_actionPerformed(boolean b)
2706 protected void redoMenuItem_actionPerformed(ActionEvent e)
2710 protected void undoMenuItem_actionPerformed(ActionEvent e)
2714 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2718 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2722 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2726 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2730 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2734 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2738 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2742 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2746 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2750 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2754 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2758 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2762 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2766 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2770 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2774 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2778 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2782 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2786 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2790 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2794 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2798 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2802 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2806 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2810 protected void clustalColour_actionPerformed(ActionEvent e)
2814 protected void zappoColour_actionPerformed(ActionEvent e)
2818 protected void taylorColour_actionPerformed(ActionEvent e)
2822 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2826 protected void helixColour_actionPerformed(ActionEvent e)
2830 protected void strandColour_actionPerformed(ActionEvent e)
2834 protected void turnColour_actionPerformed(ActionEvent e)
2838 protected void buriedColour_actionPerformed(ActionEvent e)
2842 protected void userDefinedColour_actionPerformed(ActionEvent e)
2846 protected void PIDColour_actionPerformed(ActionEvent e)
2850 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2854 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2858 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2863 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2866 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2870 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2874 protected void printMenuItem_actionPerformed(ActionEvent e)
2878 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2882 protected void findMenuItem_actionPerformed(ActionEvent e)
2886 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2890 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2894 protected void nucleotideColour_actionPerformed(ActionEvent e)
2898 protected void deleteGroups_actionPerformed(ActionEvent e)
2902 protected void createGroup_actionPerformed(ActionEvent e)
2906 protected void unGroup_actionPerformed(ActionEvent e)
2910 protected void copy_actionPerformed(ActionEvent e)
2914 protected void cut_actionPerformed(ActionEvent e)
2918 protected void delete_actionPerformed(ActionEvent e)
2922 protected void pasteNew_actionPerformed(ActionEvent e)
2926 protected void pasteThis_actionPerformed(ActionEvent e)
2930 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2934 public void createPNG(java.io.File f)
2938 protected void font_actionPerformed(ActionEvent e)
2942 protected void seqLimit_actionPerformed(ActionEvent e)
2946 public void seqDBRef_actionPerformed(ActionEvent e)
2951 public void createEPS(java.io.File f)
2955 public void createSVG(java.io.File f)
2959 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2965 * Template method to handle the 'load T-Coffee scores' menu event.
2967 * Subclasses override this method to provide a custom action.
2972 protected void loadScores_actionPerformed(ActionEvent event)
2978 * Template method to handle the 'Color T-Coffee scores' menu event.
2980 * Subclasses override this method to provide a custom action.
2985 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2990 protected void jpred_actionPerformed(ActionEvent e)
2994 protected void scaleAbove_actionPerformed(ActionEvent e)
2998 protected void scaleLeft_actionPerformed(ActionEvent e)
3002 protected void scaleRight_actionPerformed(ActionEvent e)
3006 protected void modifyPID_actionPerformed(ActionEvent e)
3010 protected void modifyConservation_actionPerformed(ActionEvent e)
3014 protected void saveAs_actionPerformed(ActionEvent e)
3018 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
3022 public void vamsasStore_actionPerformed(ActionEvent e)
3027 public void vamsasLoad_actionPerformed(ActionEvent e)
3032 public void showTranslation_actionPerformed(ActionEvent e)
3037 public void featureSettings_actionPerformed(ActionEvent e)
3042 public void fetchSequence_actionPerformed(ActionEvent e)
3047 public void smoothFont_actionPerformed(ActionEvent e)
3052 public void annotationColour_actionPerformed(ActionEvent e)
3057 public void rnahelicesColour_actionPerformed(ActionEvent e)
3062 public void associatedData_actionPerformed(ActionEvent e)
3067 public void autoCalculate_actionPerformed(ActionEvent e)
3072 public void sortByTreeOption_actionPerformed(ActionEvent e)
3077 public void showAllSeqs_actionPerformed(ActionEvent e)
3082 public void showAllColumns_actionPerformed(ActionEvent e)
3087 public void hideSelSequences_actionPerformed(ActionEvent e)
3092 public void hideSelColumns_actionPerformed(ActionEvent e)
3097 public void hiddenMarkers_actionPerformed(ActionEvent e)
3102 public void findPdbId_actionPerformed(ActionEvent e)
3107 public void enterPdbId_actionPerformed(ActionEvent e)
3112 public void pdbFile_actionPerformed(ActionEvent e)
3117 public void invertColSel_actionPerformed(ActionEvent e)
3122 public void tabSelectionChanged(int sel)
3127 public void tabbedPane_mousePressed(MouseEvent e)
3132 public void tabbedPane_focusGained(FocusEvent e)
3137 public void save_actionPerformed(ActionEvent e)
3142 public void reload_actionPerformed(ActionEvent e)
3147 public void newView_actionPerformed(ActionEvent e)
3152 public void textColour_actionPerformed(ActionEvent e)
3157 public void idRightAlign_actionPerformed(ActionEvent e)
3162 public void expandViews_actionPerformed(ActionEvent e)
3167 public void gatherViews_actionPerformed(ActionEvent e)
3172 public void buildTreeMenu()
3177 public void pageSetup_actionPerformed(ActionEvent e)
3182 public void alignmentProperties()
3187 protected void expand_newalign(ActionEvent e)
3189 // TODO Auto-generated method stub
3193 protected boolean isShowAutoCalculatedAbove()
3195 return showAutoCalculatedAbove;
3198 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3200 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3203 protected SequenceAnnotationOrder getAnnotationSortOrder()
3205 return annotationSortOrder;
3208 protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3210 this.annotationSortOrder = annotationSortOrder;
3213 public Map<KeyStroke, JMenuItem> getAccelerators()
3215 return this.accelerators;