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.MouseAdapter;
39 import java.awt.event.MouseEvent;
41 import javax.swing.BorderFactory;
42 import javax.swing.ButtonGroup;
43 import javax.swing.JCheckBoxMenuItem;
44 import javax.swing.JInternalFrame;
45 import javax.swing.JLabel;
46 import javax.swing.JMenu;
47 import javax.swing.JMenuBar;
48 import javax.swing.JMenuItem;
49 import javax.swing.JOptionPane;
50 import javax.swing.JPanel;
51 import javax.swing.JRadioButtonMenuItem;
52 import javax.swing.JTabbedPane;
53 import javax.swing.SwingUtilities;
54 import javax.swing.event.ChangeEvent;
55 import javax.swing.event.MenuEvent;
56 import javax.swing.event.MenuListener;
58 public class GAlignFrame extends JInternalFrame
60 protected JMenuBar alignFrameMenuBar = new JMenuBar();
62 protected JMenu fileMenu = new JMenu();
64 protected JMenuItem closeMenuItem = new JMenuItem();
66 protected JMenu editMenu = new JMenu();
68 protected JMenu viewMenu = new JMenu();
70 protected JMenu annotationsMenu = new JMenu();
72 protected JMenu colourMenu = new JMenu();
74 protected JMenu calculateMenu = new JMenu();
76 protected JMenu webService = new JMenu();
78 protected JMenuItem webServiceNoServices;
80 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
82 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
84 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
86 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
88 protected JMenuItem remove2RightMenuItem = new JMenuItem();
90 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
92 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
94 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
96 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
98 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
100 protected JMenuItem sortIDMenuItem = new JMenuItem();
102 protected JMenuItem sortLengthMenuItem = new JMenuItem();
104 protected JMenuItem sortGroupMenuItem = new JMenuItem();
106 protected JMenu sortByAnnotScore = new JMenu();
108 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
110 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
112 protected JMenuItem PCAMenuItem = new JMenuItem();
114 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
116 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
118 BorderLayout borderLayout1 = new BorderLayout();
120 public JLabel statusBar = new JLabel();
122 protected JMenuItem saveAs = new JMenuItem();
124 protected JMenu outputTextboxMenu = new JMenu();
126 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
144 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
146 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
148 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
150 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
152 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
154 // protected JRadioButtonMenuItem covariationColour = new
155 // JRadioButtonMenuItem();
157 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
159 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
161 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
163 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
165 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
167 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
169 JMenuItem htmlMenuItem = new JMenuItem();
171 JMenuItem overviewMenuItem = new JMenuItem();
173 protected JMenuItem undoMenuItem = new JMenuItem();
175 protected JMenuItem redoMenuItem = new JMenuItem();
177 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
179 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
181 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
183 JMenuItem printMenuItem = new JMenuItem();
185 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
187 JMenuItem findMenuItem = new JMenuItem();
189 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
191 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
193 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
195 JMenuItem deleteGroups = new JMenuItem();
197 JMenuItem createGroup = new JMenuItem();
199 JMenuItem unGroup = new JMenuItem();
201 JMenuItem delete = new JMenuItem();
203 JMenuItem copy = new JMenuItem();
205 JMenuItem cut = new JMenuItem();
207 JMenu pasteMenu = new JMenu();
209 JMenuItem pasteNew = new JMenuItem();
211 JMenuItem pasteThis = new JMenuItem();
213 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
215 JMenuItem createPNG = new JMenuItem();
217 JMenuItem createSVG = new JMenuItem();
219 protected JMenuItem font = new JMenuItem();
221 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
223 JMenuItem epsFile = new JMenuItem();
225 JMenuItem LoadtreeMenuItem = new JMenuItem();
227 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
229 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
231 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
233 protected JMenuItem modifyPID = new JMenuItem();
235 protected JMenuItem modifyConservation = new JMenuItem();
237 protected JMenu sortByTreeMenu = new JMenu();
239 protected JMenu sort = new JMenu();
241 protected JMenu calculateTree = new JMenu();
243 JMenu jMenu2 = new JMenu();
245 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
247 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
249 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
251 protected ButtonGroup colours = new ButtonGroup();
253 JMenuItem vamsasStore = new JMenuItem();
255 protected JMenuItem showTranslation = new JMenuItem();
257 protected JMenu cdna = new JMenu();
259 protected JMenuItem extractScores = new JMenuItem();
261 protected JMenuItem expandAlignment = new JMenuItem();
263 protected JMenu showProducts = new JMenu();
265 public JMenuItem openFeatureSettings = new JMenuItem();
267 JMenuItem fetchSequence = new JMenuItem();
269 JMenuItem annotationColour = new JMenuItem();
271 protected JMenuItem rnahelicesColour = new JMenuItem();
273 JMenuItem associatedData = new JMenuItem();
275 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
277 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
279 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
281 JMenu addSequenceMenu = new JMenu();
283 JMenuItem addFromFile = new JMenuItem();
285 JMenuItem addFromText = new JMenuItem();
287 JMenuItem addFromURL = new JMenuItem();
289 JMenuItem exportAnnotations = new JMenuItem();
291 JMenuItem exportFeatures = new JMenuItem();
293 protected JPanel statusPanel = new JPanel();
295 GridLayout gridLayout1 = new GridLayout();
297 JMenu jMenu3 = new JMenu();
299 JMenuItem showAllSeqs = new JMenuItem();
301 JMenuItem showAllColumns = new JMenuItem();
303 JMenu hideMenu = new JMenu();
305 JMenuItem hideSelSequences = new JMenuItem();
307 JMenuItem hideSelColumns = new JMenuItem();
309 JMenuItem hideAllButSelection = new JMenuItem();
311 JMenuItem hideAllSelection = new JMenuItem();
313 JMenuItem showAllhidden = new JMenuItem();
315 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
317 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
319 protected JMenuItem showAllAlAnnotations = new JMenuItem();
321 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
323 protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
325 protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
327 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
329 JMenuItem invertColSel = new JMenuItem();
331 protected JTabbedPane tabbedPane = new JTabbedPane();
333 JMenuItem save = new JMenuItem();
335 protected JMenuItem reload = new JMenuItem();
337 JMenuItem newView = new JMenuItem();
339 JMenuItem textColour = new JMenuItem();
341 JMenu formatMenu = new JMenu();
343 JMenu selectMenu = new JMenu();
345 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
347 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
349 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
351 protected JMenuItem gatherViews = new JMenuItem();
353 protected JMenuItem expandViews = new JMenuItem();
355 JMenuItem pageSetup = new JMenuItem();
357 JMenuItem alignmentProperties = new JMenuItem();
359 JMenu tooltipSettingsMenu = new JMenu();
361 private JMenuItem justifyLeftMenuItem = new JMenuItem();
363 private JMenuItem justifyRightMenuItem = new JMenuItem();
365 JMenu autoAnnMenu = new JMenu();
367 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
369 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
371 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
373 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
375 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
377 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
379 protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
381 protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
383 private JMenuItem grpsFromSelection = new JMenuItem();
385 private SequenceAnnotationOrder annotationSortOrder;
387 private boolean showAutoCalculatedAbove = false;
394 setJMenuBar(alignFrameMenuBar);
396 // dynamically fill save as menu with available formats
397 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
399 JMenuItem item = new JMenuItem(
400 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
402 item.addActionListener(new java.awt.event.ActionListener()
405 public void actionPerformed(ActionEvent e)
407 outputText_actionPerformed(e);
411 outputTextboxMenu.add(item);
413 } catch (Exception e)
415 System.err.println(e.toString());
418 if (!new jalview.util.Platform().isAMac())
420 closeMenuItem.setMnemonic('C');
421 outputTextboxMenu.setMnemonic('T');
422 undoMenuItem.setMnemonic('Z');
423 redoMenuItem.setMnemonic('0');
424 copy.setMnemonic('C');
425 cut.setMnemonic('U');
426 pasteMenu.setMnemonic('P');
427 reload.setMnemonic('R');
430 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
432 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
433 .getUserColourSchemes().keys();
435 while (userColours.hasMoreElements())
437 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
438 userColours.nextElement().toString());
439 radioItem.setName("USER_DEFINED");
440 radioItem.addMouseListener(new MouseAdapter()
443 public void mousePressed(MouseEvent evt)
445 if (evt.isControlDown()
446 || SwingUtilities.isRightMouseButton(evt))
448 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
450 int option = JOptionPane.showInternalConfirmDialog(
451 jalview.gui.Desktop.desktop,
453 .getString("label.remove_from_default_list"),
455 .getString("label.remove_user_defined_colour"),
456 JOptionPane.YES_NO_OPTION);
457 if (option == JOptionPane.YES_OPTION)
459 jalview.gui.UserDefinedColours
460 .removeColourFromDefaults(radioItem.getText());
461 colourMenu.remove(radioItem);
465 radioItem.addActionListener(new ActionListener()
468 public void actionPerformed(ActionEvent evt)
470 userDefinedColour_actionPerformed(evt);
477 radioItem.addActionListener(new ActionListener()
480 public void actionPerformed(ActionEvent evt)
482 userDefinedColour_actionPerformed(evt);
485 colourMenu.insert(radioItem, 15);
486 colours.add(radioItem);
489 colours.add(noColourmenuItem);
490 colours.add(clustalColour);
491 colours.add(zappoColour);
492 colours.add(taylorColour);
493 colours.add(hydrophobicityColour);
494 colours.add(helixColour);
495 colours.add(strandColour);
496 colours.add(turnColour);
497 colours.add(buriedColour);
498 colours.add(userDefinedColour);
499 colours.add(PIDColour);
500 colours.add(BLOSUM62Colour);
501 colours.add(nucleotideColour);
502 colours.add(purinePyrimidineColour);
503 // colours.add(covariationColour);
504 colours.add(tcoffeeColour);
505 colours.add(RNAInteractionColour);
506 setColourSelected(jalview.bin.Cache
507 .getDefault("DEFAULT_COLOUR", "None"));
511 public void setColourSelected(String defaultColour)
514 if (defaultColour != null)
516 int index = ColourSchemeProperty
517 .getColourIndexFromName(defaultColour);
521 case ColourSchemeProperty.CLUSTAL:
522 clustalColour.setSelected(true);
526 case ColourSchemeProperty.BLOSUM:
527 BLOSUM62Colour.setSelected(true);
531 case ColourSchemeProperty.PID:
532 PIDColour.setSelected(true);
536 case ColourSchemeProperty.ZAPPO:
537 zappoColour.setSelected(true);
541 case ColourSchemeProperty.TAYLOR:
542 taylorColour.setSelected(true);
545 case ColourSchemeProperty.HYDROPHOBIC:
546 hydrophobicityColour.setSelected(true);
550 case ColourSchemeProperty.HELIX:
551 helixColour.setSelected(true);
555 case ColourSchemeProperty.STRAND:
556 strandColour.setSelected(true);
560 case ColourSchemeProperty.TURN:
561 turnColour.setSelected(true);
565 case ColourSchemeProperty.BURIED:
566 buriedColour.setSelected(true);
570 case ColourSchemeProperty.NUCLEOTIDE:
571 nucleotideColour.setSelected(true);
575 case ColourSchemeProperty.TCOFFEE:
576 tcoffeeColour.setSelected(true);
579 case ColourSchemeProperty.PURINEPYRIMIDINE:
580 purinePyrimidineColour.setSelected(true);
584 case ColourSchemeProperty.RNAINTERACTION:
585 RNAInteractionColour.setSelected(true);
589 * case ColourSchemeProperty.COVARIATION:
590 * covariationColour.setSelected(true);
594 case ColourSchemeProperty.USER_DEFINED:
595 userDefinedColour.setSelected(true);
598 case ColourSchemeProperty.NONE:
600 noColourmenuItem.setSelected(true);
608 private void jbInit() throws Exception
610 fileMenu.setText(MessageManager.getString("action.file"));
611 saveAs.setText(MessageManager.getString("action.save_as") + "...");
612 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
613 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
614 .getMenuShortcutKeyMask()
615 | java.awt.event.KeyEvent.SHIFT_MASK, false));
616 saveAs.addActionListener(new ActionListener()
619 public void actionPerformed(ActionEvent e)
621 saveAs_actionPerformed(e);
624 closeMenuItem.setText(MessageManager.getString("action.close"));
625 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
626 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
627 .getMenuShortcutKeyMask(), false));
628 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
631 public void actionPerformed(ActionEvent e)
633 closeMenuItem_actionPerformed(false);
636 editMenu.setText(MessageManager.getString("action.edit"));
637 viewMenu.setText(MessageManager.getString("action.view"));
638 annotationsMenu.setText(MessageManager.getString("action.annotations"));
639 colourMenu.setText(MessageManager.getString("action.colour"));
640 calculateMenu.setText(MessageManager.getString("action.calculate"));
641 webService.setText(MessageManager.getString("action.web_service"));
642 selectAllSequenceMenuItem.setText(MessageManager
643 .getString("action.select_all"));
644 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
645 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
646 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
647 selectAllSequenceMenuItem
648 .addActionListener(new java.awt.event.ActionListener()
651 public void actionPerformed(ActionEvent e)
653 selectAllSequenceMenuItem_actionPerformed(e);
656 deselectAllSequenceMenuItem.setText(MessageManager
657 .getString("action.deselect_all"));
658 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
659 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
660 deselectAllSequenceMenuItem
661 .addActionListener(new java.awt.event.ActionListener()
664 public void actionPerformed(ActionEvent e)
666 deselectAllSequenceMenuItem_actionPerformed(e);
669 invertSequenceMenuItem.setText(MessageManager
670 .getString("action.invert_sequence_selection"));
671 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
672 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
673 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
674 invertSequenceMenuItem
675 .addActionListener(new java.awt.event.ActionListener()
678 public void actionPerformed(ActionEvent e)
680 invertSequenceMenuItem_actionPerformed(e);
683 grpsFromSelection.setText(MessageManager
684 .getString("action.make_groups_selection"));
685 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
688 public void actionPerformed(ActionEvent e)
690 makeGrpsFromSelection_actionPerformed(e);
693 expandAlignment.setText(MessageManager
694 .getString("action.view_flanking_regions"));
695 expandAlignment.setToolTipText(MessageManager
696 .getString("label.view_flanking_regions"));
697 expandAlignment.addActionListener(new java.awt.event.ActionListener()
700 public void actionPerformed(ActionEvent e)
705 remove2LeftMenuItem.setText(MessageManager
706 .getString("action.remove_left"));
707 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
708 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
709 .getMenuShortcutKeyMask(), false));
711 .addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 remove2LeftMenuItem_actionPerformed(e);
719 remove2RightMenuItem.setText(MessageManager
720 .getString("action.remove_right"));
721 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
722 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
723 .getMenuShortcutKeyMask(), false));
725 .addActionListener(new java.awt.event.ActionListener()
728 public void actionPerformed(ActionEvent e)
730 remove2RightMenuItem_actionPerformed(e);
733 removeGappedColumnMenuItem.setText(MessageManager
734 .getString("action.remove_empty_columns"));
735 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
736 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
737 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
738 removeGappedColumnMenuItem
739 .addActionListener(new java.awt.event.ActionListener()
742 public void actionPerformed(ActionEvent e)
744 removeGappedColumnMenuItem_actionPerformed(e);
747 removeAllGapsMenuItem.setText(MessageManager
748 .getString("action.remove_all_gaps"));
749 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
750 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
751 .getDefaultToolkit().getMenuShortcutKeyMask()
752 | java.awt.event.KeyEvent.SHIFT_MASK, false));
753 removeAllGapsMenuItem
754 .addActionListener(new java.awt.event.ActionListener()
757 public void actionPerformed(ActionEvent e)
759 removeAllGapsMenuItem_actionPerformed(e);
762 justifyLeftMenuItem.setText(MessageManager
763 .getString("action.left_justify_alignment"));
765 .addActionListener(new java.awt.event.ActionListener()
768 public void actionPerformed(ActionEvent e)
770 justifyLeftMenuItem_actionPerformed(e);
773 justifyRightMenuItem.setText(MessageManager
774 .getString("action.right_justify_alignment"));
776 .addActionListener(new java.awt.event.ActionListener()
779 public void actionPerformed(ActionEvent e)
781 justifyRightMenuItem_actionPerformed(e);
784 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
785 viewBoxesMenuItem.setState(true);
786 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
789 public void actionPerformed(ActionEvent e)
791 viewBoxesMenuItem_actionPerformed(e);
794 viewTextMenuItem.setText(MessageManager.getString("action.text"));
795 viewTextMenuItem.setState(true);
796 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
799 public void actionPerformed(ActionEvent e)
801 viewTextMenuItem_actionPerformed(e);
804 showNonconservedMenuItem.setText(MessageManager
805 .getString("label.show_non_conversed"));
806 showNonconservedMenuItem.setState(false);
807 showNonconservedMenuItem
808 .addActionListener(new java.awt.event.ActionListener()
811 public void actionPerformed(ActionEvent e)
813 showUnconservedMenuItem_actionPerformed(e);
816 sortPairwiseMenuItem.setText(MessageManager
817 .getString("action.by_pairwise_id"));
819 .addActionListener(new java.awt.event.ActionListener()
822 public void actionPerformed(ActionEvent e)
824 sortPairwiseMenuItem_actionPerformed(e);
827 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
828 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
831 public void actionPerformed(ActionEvent e)
833 sortIDMenuItem_actionPerformed(e);
837 .setText(MessageManager.getString("action.by_length"));
839 .addActionListener(new java.awt.event.ActionListener()
842 public void actionPerformed(ActionEvent e)
844 sortLengthMenuItem_actionPerformed(e);
847 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
848 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
851 public void actionPerformed(ActionEvent e)
853 sortGroupMenuItem_actionPerformed(e);
856 removeRedundancyMenuItem.setText(MessageManager
857 .getString("action.remove_redundancy").concat("..."));
858 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
859 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
860 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
861 removeRedundancyMenuItem
862 .addActionListener(new java.awt.event.ActionListener()
865 public void actionPerformed(ActionEvent e)
867 removeRedundancyMenuItem_actionPerformed(e);
870 pairwiseAlignmentMenuItem.setText(MessageManager
871 .getString("action.pairwise_alignment"));
872 pairwiseAlignmentMenuItem
873 .addActionListener(new java.awt.event.ActionListener()
876 public void actionPerformed(ActionEvent e)
878 pairwiseAlignmentMenuItem_actionPerformed(e);
881 PCAMenuItem.setText(MessageManager
882 .getString("label.principal_component_analysis"));
883 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
886 public void actionPerformed(ActionEvent e)
888 PCAMenuItem_actionPerformed(e);
891 averageDistanceTreeMenuItem.setText(MessageManager
892 .getString("label.average_distance_identity"));
893 averageDistanceTreeMenuItem
894 .addActionListener(new java.awt.event.ActionListener()
897 public void actionPerformed(ActionEvent e)
899 averageDistanceTreeMenuItem_actionPerformed(e);
902 neighbourTreeMenuItem.setText(MessageManager
903 .getString("label.neighbour_joining_identity"));
904 neighbourTreeMenuItem
905 .addActionListener(new java.awt.event.ActionListener()
908 public void actionPerformed(ActionEvent e)
910 neighbourTreeMenuItem_actionPerformed(e);
913 this.getContentPane().setLayout(borderLayout1);
914 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
915 statusBar.setBackground(Color.white);
916 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
917 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
918 statusBar.setText(MessageManager.getString("label.status_bar"));
919 outputTextboxMenu.setText(MessageManager
920 .getString("label.out_to_textbox"));
921 clustalColour.setText(MessageManager.getString("label.clustalx"));
923 clustalColour.addActionListener(new java.awt.event.ActionListener()
926 public void actionPerformed(ActionEvent e)
928 clustalColour_actionPerformed(e);
931 zappoColour.setText(MessageManager.getString("label.zappo"));
932 zappoColour.addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 zappoColour_actionPerformed(e);
940 taylorColour.setText(MessageManager.getString("label.taylor"));
941 taylorColour.addActionListener(new java.awt.event.ActionListener()
944 public void actionPerformed(ActionEvent e)
946 taylorColour_actionPerformed(e);
949 hydrophobicityColour.setText(MessageManager
950 .getString("label.hydrophobicity"));
952 .addActionListener(new java.awt.event.ActionListener()
955 public void actionPerformed(ActionEvent e)
957 hydrophobicityColour_actionPerformed(e);
960 helixColour.setText(MessageManager.getString("label.helix_propensity"));
961 helixColour.addActionListener(new java.awt.event.ActionListener()
964 public void actionPerformed(ActionEvent e)
966 helixColour_actionPerformed(e);
969 strandColour.setText(MessageManager
970 .getString("label.strand_propensity"));
971 strandColour.addActionListener(new java.awt.event.ActionListener()
974 public void actionPerformed(ActionEvent e)
976 strandColour_actionPerformed(e);
979 turnColour.setText(MessageManager.getString("label.turn_propensity"));
980 turnColour.addActionListener(new java.awt.event.ActionListener()
983 public void actionPerformed(ActionEvent e)
985 turnColour_actionPerformed(e);
988 buriedColour.setText(MessageManager.getString("label.buried_index"));
989 buriedColour.addActionListener(new java.awt.event.ActionListener()
992 public void actionPerformed(ActionEvent e)
994 buriedColour_actionPerformed(e);
997 userDefinedColour.setText(MessageManager
998 .getString("action.user_defined"));
999 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1002 public void actionPerformed(ActionEvent e)
1004 userDefinedColour_actionPerformed(e);
1008 .setText(MessageManager.getString("label.percentage_identity"));
1009 PIDColour.addActionListener(new java.awt.event.ActionListener()
1012 public void actionPerformed(ActionEvent e)
1014 PIDColour_actionPerformed(e);
1018 .setText(MessageManager.getString("label.blosum62_score"));
1019 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1022 public void actionPerformed(ActionEvent e)
1024 BLOSUM62Colour_actionPerformed(e);
1027 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1028 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 nucleotideColour_actionPerformed(e);
1037 purinePyrimidineColour.setText(MessageManager
1038 .getString("label.purine_pyrimidine"));
1039 purinePyrimidineColour
1040 .addActionListener(new java.awt.event.ActionListener()
1043 public void actionPerformed(ActionEvent e)
1045 purinePyrimidineColour_actionPerformed(e);
1049 RNAInteractionColour.setText("RNA Interaction type");
1050 RNAInteractionColour
1051 .addActionListener(new java.awt.event.ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 RNAInteractionColour_actionPerformed(e);
1060 * covariationColour.setText("Covariation");
1061 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1062 * public void actionPerformed(ActionEvent e) {
1063 * covariationColour_actionPerformed(e); } });
1066 avDistanceTreeBlosumMenuItem.setText(MessageManager
1067 .getString("label.average_distance_bloslum62"));
1068 avDistanceTreeBlosumMenuItem
1069 .addActionListener(new java.awt.event.ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 avTreeBlosumMenuItem_actionPerformed(e);
1077 njTreeBlosumMenuItem.setText(MessageManager
1078 .getString("label.neighbour_blosum62"));
1079 njTreeBlosumMenuItem
1080 .addActionListener(new java.awt.event.ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 njTreeBlosumMenuItem_actionPerformed(e);
1088 annotationPanelMenuItem.setActionCommand("");
1089 annotationPanelMenuItem.setText(MessageManager
1090 .getString("label.show_annotations"));
1091 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1093 annotationPanelMenuItem.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent e)
1098 annotationPanelMenuItem_actionPerformed(e);
1101 showAllAlAnnotations.setText(MessageManager
1102 .getString("label.show_all_al_annotations"));
1103 final boolean isAnnotationPanelShown = annotationPanelMenuItem
1105 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1106 showAllAlAnnotations.addActionListener(new ActionListener()
1109 public void actionPerformed(ActionEvent e)
1111 showAllAnnotations_actionPerformed(false, true);
1114 hideAllAlAnnotations.setText(MessageManager
1115 .getString("label.hide_all_al_annotations"));
1116 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1117 hideAllAlAnnotations.addActionListener(new ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 hideAllAnnotations_actionPerformed(false, true);
1125 showAllSeqAnnotations.setText(MessageManager
1126 .getString("label.show_all_seq_annotations"));
1127 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1128 showAllSeqAnnotations.addActionListener(new ActionListener()
1131 public void actionPerformed(ActionEvent e)
1133 showAllAnnotations_actionPerformed(true, false);
1136 hideAllSeqAnnotations.setText(MessageManager
1137 .getString("label.hide_all_seq_annotations"));
1138 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1139 hideAllSeqAnnotations.addActionListener(new ActionListener()
1142 public void actionPerformed(ActionEvent e)
1144 hideAllAnnotations_actionPerformed(true, false);
1147 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1148 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
1149 SequenceAnnotationOrder.NONE.name()));
1150 sortAnnBySequence.setText(MessageManager
1151 .getString("label.sort_annotations_by_sequence"));
1153 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1154 sortAnnBySequence.addActionListener(new ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 boolean newState = sortAnnBySequence.getState();
1160 sortAnnByLabel.setSelected(false);
1161 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1162 : SequenceAnnotationOrder.NONE);
1163 sortAnnotations_actionPerformed();
1166 sortAnnByLabel.setText(MessageManager
1167 .getString("label.sort_annotations_by_label"));
1169 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1170 sortAnnByLabel.addActionListener(new ActionListener()
1173 public void actionPerformed(ActionEvent e)
1175 boolean newState = sortAnnByLabel.getState();
1176 sortAnnBySequence.setSelected(false);
1177 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1178 : SequenceAnnotationOrder.NONE);
1179 sortAnnotations_actionPerformed();
1182 colourTextMenuItem.setText(MessageManager
1183 .getString("label.colour_text"));
1185 .addActionListener(new java.awt.event.ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 colourTextMenuItem_actionPerformed(e);
1193 htmlMenuItem.setText(MessageManager.getString("label.html"));
1194 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 htmlMenuItem_actionPerformed(e);
1202 overviewMenuItem.setText(MessageManager
1203 .getString("label.overview_window"));
1204 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 overviewMenuItem_actionPerformed(e);
1212 undoMenuItem.setEnabled(false);
1213 undoMenuItem.setText(MessageManager.getString("action.undo"));
1214 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1215 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1216 .getMenuShortcutKeyMask(), false));
1217 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 undoMenuItem_actionPerformed(e);
1225 redoMenuItem.setEnabled(false);
1226 redoMenuItem.setText(MessageManager.getString("action.redo"));
1227 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1228 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1229 .getMenuShortcutKeyMask(), false));
1230 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1233 public void actionPerformed(ActionEvent e)
1235 redoMenuItem_actionPerformed(e);
1238 conservationMenuItem.setText(MessageManager
1239 .getString("action.by_conservation"));
1240 conservationMenuItem
1241 .addActionListener(new java.awt.event.ActionListener()
1244 public void actionPerformed(ActionEvent e)
1246 conservationMenuItem_actionPerformed(e);
1249 noColourmenuItem.setText(MessageManager.getString("label.none"));
1250 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1253 public void actionPerformed(ActionEvent e)
1255 noColourmenuItem_actionPerformed(e);
1258 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1259 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 wrapMenuItem_actionPerformed(e);
1267 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1268 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1269 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1270 .getMenuShortcutKeyMask(), false));
1271 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1274 public void actionPerformed(ActionEvent e)
1276 printMenuItem_actionPerformed(e);
1280 .setText(MessageManager.getString("action.show_gaps"));
1281 renderGapsMenuItem.setState(true);
1283 .addActionListener(new java.awt.event.ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 renderGapsMenuItem_actionPerformed(e);
1291 findMenuItem.setText(MessageManager.getString("action.find"));
1292 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1293 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1294 .getMenuShortcutKeyMask(), false));
1295 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1296 MessageManager.getString("label.find_tip")));
1297 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 findMenuItem_actionPerformed(e);
1305 abovePIDThreshold.setText(MessageManager
1306 .getString("label.above_identity_threshold"));
1307 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1310 public void actionPerformed(ActionEvent e)
1312 abovePIDThreshold_actionPerformed(e);
1315 showSeqFeatures.setText(MessageManager
1316 .getString("label.show_sequence_features"));
1317 showSeqFeatures.addActionListener(new ActionListener()
1320 public void actionPerformed(ActionEvent actionEvent)
1322 showSeqFeatures_actionPerformed(actionEvent);
1326 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1327 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1328 * void actionPerformed(ActionEvent actionEvent) {
1329 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1331 showDbRefsMenuitem.setText(MessageManager
1332 .getString("label.show_database_refs"));
1333 showDbRefsMenuitem.addActionListener(new ActionListener()
1337 public void actionPerformed(ActionEvent e)
1339 showDbRefs_actionPerformed(e);
1343 showNpFeatsMenuitem.setText(MessageManager
1344 .getString("label.show_non_positional_features"));
1345 showNpFeatsMenuitem.addActionListener(new ActionListener()
1349 public void actionPerformed(ActionEvent e)
1351 showNpFeats_actionPerformed(e);
1355 showGroupConservation.setText(MessageManager
1356 .getString("label.group_conservation"));
1357 showGroupConservation.addActionListener(new ActionListener()
1361 public void actionPerformed(ActionEvent e)
1363 showGroupConservation_actionPerformed(e);
1368 showGroupConsensus.setText(MessageManager
1369 .getString("label.group_consensus"));
1370 showGroupConsensus.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 showGroupConsensus_actionPerformed(e);
1380 showConsensusHistogram.setText(MessageManager
1381 .getString("label.show_consensus_histogram"));
1382 showConsensusHistogram.addActionListener(new ActionListener()
1386 public void actionPerformed(ActionEvent e)
1388 showConsensusHistogram_actionPerformed(e);
1392 showSequenceLogo.setText(MessageManager
1393 .getString("label.show_consensus_logo"));
1394 showSequenceLogo.addActionListener(new ActionListener()
1398 public void actionPerformed(ActionEvent e)
1400 showSequenceLogo_actionPerformed(e);
1404 normaliseSequenceLogo.setText(MessageManager
1405 .getString("label.norm_consensus_logo"));
1406 normaliseSequenceLogo.addActionListener(new ActionListener()
1410 public void actionPerformed(ActionEvent e)
1412 normaliseSequenceLogo_actionPerformed(e);
1416 applyAutoAnnotationSettings.setText(MessageManager
1417 .getString("label.apply_all_groups"));
1418 applyAutoAnnotationSettings.setState(false);
1419 applyAutoAnnotationSettings.setVisible(true);
1420 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1423 public void actionPerformed(ActionEvent e)
1425 applyAutoAnnotationSettings_actionPerformed(e);
1429 ButtonGroup buttonGroup = new ButtonGroup();
1430 buttonGroup.add(showAutoFirst);
1431 buttonGroup.add(showAutoLast);
1432 showAutoFirst.setText(MessageManager.getString("label.show_first"));
1433 showAutoFirst.setSelected(Cache.getDefault(
1434 Preferences.SHOW_AUTOCALC_ABOVE,
1436 showAutoFirst.addActionListener(new ActionListener()
1439 public void actionPerformed(ActionEvent e)
1441 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1442 sortAnnotations_actionPerformed();
1445 showAutoLast.setText(MessageManager.getString("label.show_last"));
1446 showAutoLast.setSelected(!showAutoFirst.isSelected());
1447 showAutoLast.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1453 sortAnnotations_actionPerformed();
1457 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1458 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 nucleotideColour_actionPerformed(e);
1467 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1468 tcoffeeColour.setEnabled(false);
1469 tcoffeeColour.addActionListener(new ActionListener()
1473 public void actionPerformed(ActionEvent e)
1475 tcoffeeColorScheme_actionPerformed(e);
1480 .setText(MessageManager.getString("action.undefine_groups"));
1481 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1482 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1483 .getMenuShortcutKeyMask(), false));
1484 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1487 public void actionPerformed(ActionEvent e)
1489 deleteGroups_actionPerformed(e);
1492 createGroup.setText(MessageManager.getString("action.create_groups"));
1493 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1494 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1495 .getMenuShortcutKeyMask(), false));
1496 createGroup.addActionListener(new java.awt.event.ActionListener()
1499 public void actionPerformed(ActionEvent e)
1501 createGroup_actionPerformed(e);
1504 unGroup.setText(MessageManager.getString("action.remove_group"));
1505 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1506 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1507 .getMenuShortcutKeyMask()
1508 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1509 unGroup.addActionListener(new java.awt.event.ActionListener()
1512 public void actionPerformed(ActionEvent e)
1514 unGroup_actionPerformed(e);
1517 copy.setText(MessageManager.getString("action.copy"));
1518 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1519 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1520 .getMenuShortcutKeyMask(), false));
1522 copy.addActionListener(new java.awt.event.ActionListener()
1525 public void actionPerformed(ActionEvent e)
1527 copy_actionPerformed(e);
1530 cut.setText(MessageManager.getString("action.cut"));
1531 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1532 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1533 .getMenuShortcutKeyMask(), false));
1534 cut.addActionListener(new java.awt.event.ActionListener()
1537 public void actionPerformed(ActionEvent e)
1539 cut_actionPerformed(e);
1542 delete.setText(MessageManager.getString("action.delete"));
1543 delete.addActionListener(new java.awt.event.ActionListener()
1546 public void actionPerformed(ActionEvent e)
1548 delete_actionPerformed(e);
1551 pasteMenu.setText(MessageManager.getString("action.paste"));
1552 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1553 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1554 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1555 .getMenuShortcutKeyMask()
1556 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1557 pasteNew.addActionListener(new java.awt.event.ActionListener()
1560 public void actionPerformed(ActionEvent e)
1562 pasteNew_actionPerformed(e);
1565 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1566 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1567 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1568 .getMenuShortcutKeyMask(), false));
1569 pasteThis.addActionListener(new java.awt.event.ActionListener()
1572 public void actionPerformed(ActionEvent e)
1574 pasteThis_actionPerformed(e);
1577 applyToAllGroups.setText(MessageManager
1578 .getString("label.apply_colour_to_all_groups"));
1579 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 applyToAllGroups_actionPerformed(e);
1587 createPNG.addActionListener(new java.awt.event.ActionListener()
1590 public void actionPerformed(ActionEvent e)
1595 createPNG.setActionCommand(MessageManager
1596 .getString("label.save_png_image"));
1597 createPNG.setText("PNG");
1599 font.setText(MessageManager.getString("action.font"));
1600 font.addActionListener(new java.awt.event.ActionListener()
1603 public void actionPerformed(ActionEvent e)
1605 font_actionPerformed(e);
1609 seqLimits.setText(MessageManager
1610 .getString("label.show_sequence_limits"));
1611 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1612 seqLimits.addActionListener(new java.awt.event.ActionListener()
1615 public void actionPerformed(ActionEvent e)
1617 seqLimit_actionPerformed(e);
1620 epsFile.setText("EPS");
1621 epsFile.addActionListener(new java.awt.event.ActionListener()
1624 public void actionPerformed(ActionEvent e)
1630 createSVG.setText("SVG");
1631 createSVG.addActionListener(new java.awt.event.ActionListener()
1634 public void actionPerformed(ActionEvent e)
1640 LoadtreeMenuItem.setActionCommand(MessageManager
1641 .getString("label.load_tree_for_sequence_set"));
1642 LoadtreeMenuItem.setText(MessageManager
1643 .getString("label.load_associated_tree"));
1644 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1647 public void actionPerformed(ActionEvent e)
1649 LoadtreeMenuItem_actionPerformed(e);
1653 scaleAbove.setVisible(false);
1654 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1655 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1658 public void actionPerformed(ActionEvent e)
1660 scaleAbove_actionPerformed(e);
1663 scaleLeft.setVisible(false);
1664 scaleLeft.setSelected(true);
1665 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1666 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1669 public void actionPerformed(ActionEvent e)
1671 scaleLeft_actionPerformed(e);
1674 scaleRight.setVisible(false);
1675 scaleRight.setSelected(true);
1676 scaleRight.setText(MessageManager.getString("action.scale_right"));
1677 scaleRight.addActionListener(new java.awt.event.ActionListener()
1680 public void actionPerformed(ActionEvent e)
1682 scaleRight_actionPerformed(e);
1685 centreColumnLabelsMenuItem.setVisible(true);
1686 centreColumnLabelsMenuItem.setState(false);
1687 centreColumnLabelsMenuItem.setText(MessageManager
1688 .getString("label.centre_column_labels"));
1689 centreColumnLabelsMenuItem
1690 .addActionListener(new java.awt.event.ActionListener()
1693 public void actionPerformed(ActionEvent e)
1695 centreColumnLabels_actionPerformed(e);
1698 followHighlightMenuItem.setVisible(true);
1699 followHighlightMenuItem.setState(true);
1700 followHighlightMenuItem.setText(MessageManager
1701 .getString("label.automatic_scrolling"));
1702 followHighlightMenuItem.addActionListener(new ActionListener()
1706 public void actionPerformed(ActionEvent e)
1708 followHighlight_actionPerformed();
1713 modifyPID.setText(MessageManager
1714 .getString("label.modify_identity_thereshold"));
1715 modifyPID.addActionListener(new java.awt.event.ActionListener()
1718 public void actionPerformed(ActionEvent e)
1720 modifyPID_actionPerformed(e);
1723 modifyConservation.setText(MessageManager
1724 .getString("label.modify_conservation_thereshold"));
1726 .addActionListener(new java.awt.event.ActionListener()
1729 public void actionPerformed(ActionEvent e)
1731 modifyConservation_actionPerformed(e);
1735 .setText(MessageManager.getString("action.by_tree_order"));
1736 sort.setText(MessageManager.getString("action.sort"));
1737 sort.addMenuListener(new MenuListener()
1740 public void menuSelected(MenuEvent e)
1746 public void menuDeselected(MenuEvent e)
1751 public void menuCanceled(MenuEvent e)
1755 sortByAnnotScore.setText(MessageManager
1756 .getString("label.sort_by_score"));
1757 sort.add(sortByAnnotScore);
1758 sort.addMenuListener(new javax.swing.event.MenuListener()
1762 public void menuCanceled(MenuEvent e)
1767 public void menuDeselected(MenuEvent e)
1772 public void menuSelected(MenuEvent e)
1774 buildSortByAnnotationScoresMenu();
1777 sortByAnnotScore.setVisible(false);
1780 .setText(MessageManager.getString("action.calculate_tree"));
1782 jMenu2.setText(MessageManager.getString("label.export_image"));
1783 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1784 padGapsMenuitem.setState(jalview.bin.Cache
1785 .getDefault("PAD_GAPS", false));
1786 padGapsMenuitem.addActionListener(new ActionListener()
1789 public void actionPerformed(ActionEvent e)
1791 padGapsMenuitem_actionPerformed(e);
1794 vamsasStore.setVisible(false);
1795 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1796 vamsasStore.addActionListener(new ActionListener()
1799 public void actionPerformed(ActionEvent e)
1801 vamsasStore_actionPerformed(e);
1804 showTranslation.setText(MessageManager
1805 .getString("label.translate_cDNA"));
1806 showTranslation.addActionListener(new ActionListener()
1809 public void actionPerformed(ActionEvent e)
1811 showTranslation_actionPerformed(e);
1818 cdna.setText(MessageManager.getString("label.cdna"));
1819 // link to available cDNA
1820 JMenuItem linkCdna = new JMenuItem(
1821 MessageManager.getString("label.link_cdna"));
1822 linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1823 MessageManager.getString("label.link_cdna_tip")));
1824 linkCdna.addActionListener(new ActionListener()
1827 public void actionPerformed(ActionEvent e)
1829 linkCdna_actionPerformed();
1833 // align linked cDNA
1834 JMenuItem alignCdna = new JMenuItem(
1835 MessageManager.getString("label.align_cdna"));
1836 alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1837 MessageManager.getString("label.align_cdna_tip")));
1838 alignCdna.addActionListener(new ActionListener()
1841 public void actionPerformed(ActionEvent e)
1843 alignCdna_actionPerformed();
1846 cdna.add(alignCdna);
1848 // view alignment as cDNA (when known)
1849 JMenuItem viewAsCdna = new JMenuItem(
1850 MessageManager.getString("label.view_as_cdna"));
1851 viewAsCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
1852 MessageManager.getString("label.view_as_cdna_tip")));
1853 viewAsCdna.addActionListener(new ActionListener() {
1855 public void actionPerformed(ActionEvent e)
1857 viewAsCdna_actionPerformed();
1860 cdna.add(viewAsCdna);
1862 extractScores.setText(MessageManager.getString("label.extract_scores")
1864 extractScores.addActionListener(new ActionListener()
1867 public void actionPerformed(ActionEvent e)
1869 extractScores_actionPerformed(e);
1872 extractScores.setVisible(true);
1873 // JBPNote: TODO: make gui for regex based score extraction
1875 // for show products actions see AlignFrame.canShowProducts
1876 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1877 openFeatureSettings.setText(MessageManager
1878 .getString("label.feature_settings"));
1879 openFeatureSettings.addActionListener(new ActionListener()
1882 public void actionPerformed(ActionEvent e)
1884 featureSettings_actionPerformed(e);
1888 .setText(MessageManager.getString("label.fetch_sequences"));
1889 fetchSequence.addActionListener(new ActionListener()
1892 public void actionPerformed(ActionEvent e)
1894 fetchSequence_actionPerformed(e);
1898 annotationColour.setText(MessageManager
1899 .getString("action.by_annotation"));
1900 annotationColour.addActionListener(new ActionListener()
1903 public void actionPerformed(ActionEvent e)
1905 annotationColour_actionPerformed(e);
1909 rnahelicesColour.setText(MessageManager
1910 .getString("action.by_rna_helixes"));
1911 rnahelicesColour.addActionListener(new ActionListener()
1914 public void actionPerformed(ActionEvent e)
1916 rnahelicesColour_actionPerformed(e);
1920 associatedData.setText(MessageManager
1921 .getString("label.load_features_annotations"));
1922 associatedData.addActionListener(new ActionListener()
1925 public void actionPerformed(ActionEvent e)
1927 associatedData_actionPerformed(e);
1930 autoCalculate.setText(MessageManager
1931 .getString("label.autocalculate_consensus"));
1932 autoCalculate.setState(jalview.bin.Cache.getDefault(
1933 "AUTO_CALC_CONSENSUS", true));
1934 autoCalculate.addActionListener(new ActionListener()
1937 public void actionPerformed(ActionEvent e)
1939 autoCalculate_actionPerformed(e);
1942 sortByTree.setText(MessageManager
1943 .getString("label.sort_alignment_new_tree"));
1945 .setToolTipText("<html>"
1947 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1949 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1950 sortByTree.addActionListener(new ActionListener()
1953 public void actionPerformed(ActionEvent e)
1955 sortByTreeOption_actionPerformed(e);
1959 listenToViewSelections.setText(MessageManager
1960 .getString("label.listen_for_selections"));
1961 listenToViewSelections
1962 .setToolTipText("<html>"
1964 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1965 listenToViewSelections.setState(false);
1966 listenToViewSelections.addActionListener(new ActionListener()
1969 public void actionPerformed(ActionEvent e)
1971 listenToViewSelections_actionPerformed(e);
1976 .setText(MessageManager.getString("label.add_sequences"));
1977 addFromFile.setText(MessageManager.getString("label.from_file"));
1978 addFromFile.addActionListener(new ActionListener()
1981 public void actionPerformed(ActionEvent e)
1983 addFromFile_actionPerformed(e);
1986 addFromText.setText(MessageManager.getString("label.from_textbox"));
1987 addFromText.addActionListener(new ActionListener()
1990 public void actionPerformed(ActionEvent e)
1992 addFromText_actionPerformed(e);
1995 addFromURL.setText(MessageManager.getString("label.from_url"));
1996 addFromURL.addActionListener(new ActionListener()
1999 public void actionPerformed(ActionEvent e)
2001 addFromURL_actionPerformed(e);
2004 exportFeatures.setText(MessageManager
2005 .getString("label.export_features"));
2006 exportFeatures.addActionListener(new ActionListener()
2009 public void actionPerformed(ActionEvent e)
2011 exportFeatures_actionPerformed(e);
2014 exportAnnotations.setText(MessageManager
2015 .getString("label.export_annotations"));
2016 exportAnnotations.addActionListener(new ActionListener()
2019 public void actionPerformed(ActionEvent e)
2021 exportAnnotations_actionPerformed(e);
2024 statusPanel.setLayout(gridLayout1);
2025 jMenu3.setText(MessageManager.getString("action.show"));
2026 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
2027 showAllSeqs.setToolTipText(MessageManager
2028 .getString("label.toggle_sequence_visibility"));
2029 showAllSeqs.addActionListener(new ActionListener()
2032 public void actionPerformed(ActionEvent e)
2034 showAllSeqs_actionPerformed(e);
2037 showAllColumns.setText(MessageManager.getString("label.all_columns"));
2038 showAllColumns.setToolTipText(MessageManager
2039 .getString("label.toggle_columns_visibility"));
2040 showAllColumns.addActionListener(new ActionListener()
2043 public void actionPerformed(ActionEvent e)
2045 showAllColumns_actionPerformed(e);
2048 hideMenu.setText(MessageManager.getString("action.hide"));
2049 hideSelSequences.setText(MessageManager
2050 .getString("label.selected_sequences"));
2051 hideSelSequences.setToolTipText(MessageManager
2052 .getString("label.toggle_sequence_visibility"));
2053 hideSelSequences.addActionListener(new ActionListener()
2056 public void actionPerformed(ActionEvent e)
2058 hideSelSequences_actionPerformed(e);
2061 hideSelColumns.setText(MessageManager
2062 .getString("label.selected_columns"));
2063 hideSelColumns.setToolTipText(MessageManager
2064 .getString("label.toggle_columns_visibility"));
2065 hideSelColumns.addActionListener(new ActionListener()
2068 public void actionPerformed(ActionEvent e)
2070 hideSelColumns_actionPerformed(e);
2073 hideAllSelection.setText(MessageManager
2074 .getString("label.selected_region"));
2075 hideAllSelection.addActionListener(new ActionListener()
2078 public void actionPerformed(ActionEvent e)
2080 hideAllSelection_actionPerformed(e);
2083 // TODO: should be hidden if no selection exists.
2084 hideAllButSelection.setText(MessageManager
2085 .getString("label.all_but_selected_region"));
2086 hideAllButSelection.addActionListener(new ActionListener()
2089 public void actionPerformed(ActionEvent e)
2091 hideAllButSelection_actionPerformed(e);
2094 showAllhidden.setText(MessageManager
2095 .getString("label.all_sequences_columns"));
2096 showAllhidden.setToolTipText(MessageManager
2097 .getString("label.toggles_visibility_hidden_selected_regions"));
2098 showAllhidden.addActionListener(new ActionListener()
2101 public void actionPerformed(ActionEvent e)
2103 showAllhidden_actionPerformed(e);
2106 hiddenMarkers.setText(MessageManager
2107 .getString("action.show_hidden_markers"));
2108 hiddenMarkers.addActionListener(new ActionListener()
2111 public void actionPerformed(ActionEvent e)
2113 hiddenMarkers_actionPerformed(e);
2116 invertColSel.setText(MessageManager
2117 .getString("action.invert_column_selection"));
2118 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2119 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2120 .getMenuShortcutKeyMask()
2121 | java.awt.event.KeyEvent.ALT_MASK, false));
2122 invertColSel.addActionListener(new ActionListener()
2125 public void actionPerformed(ActionEvent e)
2127 invertColSel_actionPerformed(e);
2130 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2133 public void stateChanged(ChangeEvent evt)
2135 JTabbedPane pane = (JTabbedPane) evt.getSource();
2136 int sel = pane.getSelectedIndex();
2137 tabSelectionChanged(sel);
2140 tabbedPane.addMouseListener(new MouseAdapter()
2143 public void mousePressed(MouseEvent e)
2145 tabbedPane_mousePressed(e);
2148 tabbedPane.addFocusListener(new FocusAdapter()
2151 public void focusGained(FocusEvent e)
2153 tabbedPane_focusGained(e);
2156 save.setText(MessageManager.getString("action.save"));
2157 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2158 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2159 .getMenuShortcutKeyMask(), false));
2160 save.addActionListener(new ActionListener()
2163 public void actionPerformed(ActionEvent e)
2165 save_actionPerformed(e);
2168 reload.setEnabled(false);
2169 reload.setText(MessageManager.getString("action.reload"));
2170 reload.addActionListener(new ActionListener()
2173 public void actionPerformed(ActionEvent e)
2175 reload_actionPerformed(e);
2178 newView.setText(MessageManager.getString("action.new_view"));
2179 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2180 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2181 .getMenuShortcutKeyMask(), false));
2182 newView.addActionListener(new ActionListener()
2185 public void actionPerformed(ActionEvent e)
2187 newView_actionPerformed(e);
2190 tabbedPane.setToolTipText("<html><i>"
2191 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2193 textColour.setText(MessageManager.getString("label.colour_text")
2195 textColour.addActionListener(new ActionListener()
2198 public void actionPerformed(ActionEvent e)
2200 textColour_actionPerformed(e);
2203 formatMenu.setText(MessageManager.getString("action.format"));
2204 selectMenu.setText(MessageManager.getString("action.select"));
2205 idRightAlign.setText(MessageManager
2206 .getString("label.right_align_sequence_id"));
2207 idRightAlign.addActionListener(new ActionListener()
2210 public void actionPerformed(ActionEvent e)
2212 idRightAlign_actionPerformed(e);
2215 gatherViews.setEnabled(false);
2216 gatherViews.setText(MessageManager.getString("action.gather_views"));
2217 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2218 java.awt.event.KeyEvent.VK_G, 0, false));
2219 gatherViews.addActionListener(new ActionListener()
2222 public void actionPerformed(ActionEvent e)
2224 gatherViews_actionPerformed(e);
2227 expandViews.setEnabled(false);
2228 expandViews.setText(MessageManager.getString("action.expand_views"));
2229 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2230 java.awt.event.KeyEvent.VK_X, 0, false));
2231 expandViews.addActionListener(new ActionListener()
2234 public void actionPerformed(ActionEvent e)
2236 expandViews_actionPerformed(e);
2240 .setText(MessageManager.getString("action.page_setup") + "...");
2241 pageSetup.addActionListener(new ActionListener()
2244 public void actionPerformed(ActionEvent e)
2246 pageSetup_actionPerformed(e);
2249 alignmentProperties.setText(MessageManager
2250 .getString("label.alignment_props") + "...");
2251 alignmentProperties.addActionListener(new ActionListener()
2254 public void actionPerformed(ActionEvent actionEvent)
2256 alignmentProperties();
2259 tooltipSettingsMenu.setText(MessageManager
2260 .getString("label.sequence_id_tooltip"));
2261 autoAnnMenu.setText(MessageManager
2262 .getString("label.autocalculated_annotation"));
2263 alignFrameMenuBar.add(fileMenu);
2264 alignFrameMenuBar.add(editMenu);
2265 alignFrameMenuBar.add(selectMenu);
2266 alignFrameMenuBar.add(viewMenu);
2267 alignFrameMenuBar.add(annotationsMenu);
2268 alignFrameMenuBar.add(formatMenu);
2269 alignFrameMenuBar.add(colourMenu);
2270 alignFrameMenuBar.add(calculateMenu);
2271 alignFrameMenuBar.add(webService);
2272 fileMenu.add(fetchSequence);
2273 fileMenu.add(addSequenceMenu);
2274 fileMenu.add(reload);
2275 fileMenu.addSeparator();
2276 fileMenu.add(vamsasStore);
2278 fileMenu.add(saveAs);
2279 fileMenu.add(outputTextboxMenu);
2280 fileMenu.add(pageSetup);
2281 fileMenu.add(printMenuItem);
2282 fileMenu.addSeparator();
2283 fileMenu.add(jMenu2);
2284 fileMenu.add(exportFeatures);
2285 fileMenu.add(exportAnnotations);
2286 fileMenu.add(LoadtreeMenuItem);
2287 fileMenu.add(associatedData);
2288 fileMenu.addSeparator();
2289 fileMenu.add(closeMenuItem);
2290 editMenu.add(undoMenuItem);
2291 editMenu.add(redoMenuItem);
2294 editMenu.add(pasteMenu);
2295 editMenu.add(delete);
2296 editMenu.addSeparator();
2297 editMenu.add(remove2LeftMenuItem);
2298 editMenu.add(remove2RightMenuItem);
2299 editMenu.add(removeGappedColumnMenuItem);
2300 editMenu.add(removeAllGapsMenuItem);
2301 editMenu.add(removeRedundancyMenuItem);
2302 editMenu.addSeparator();
2303 // dont add these yet in the CVS build - they cannot be undone!
2304 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2305 // editMenu.add(justifyLeftMenuItem);
2306 // editMenu.add(justifyRightMenuItem);
2307 // editMenu.addSeparator();
2308 editMenu.add(padGapsMenuitem);
2309 viewMenu.add(newView);
2310 viewMenu.add(expandViews);
2311 viewMenu.add(gatherViews);
2312 viewMenu.addSeparator();
2313 viewMenu.add(jMenu3);
2314 viewMenu.add(hideMenu);
2315 viewMenu.addSeparator();
2316 viewMenu.add(followHighlightMenuItem);
2317 annotationsMenu.add(annotationPanelMenuItem);
2318 annotationsMenu.addSeparator();
2319 annotationsMenu.add(showAllAlAnnotations);
2320 annotationsMenu.add(hideAllAlAnnotations);
2321 annotationsMenu.addSeparator();
2322 annotationsMenu.add(showAllSeqAnnotations);
2323 annotationsMenu.add(hideAllSeqAnnotations);
2324 annotationsMenu.add(sortAnnBySequence);
2325 annotationsMenu.add(sortAnnByLabel);
2326 annotationsMenu.addSeparator();
2327 autoAnnMenu.add(showAutoFirst);
2328 autoAnnMenu.add(showAutoLast);
2329 autoAnnMenu.addSeparator();
2330 autoAnnMenu.add(applyAutoAnnotationSettings);
2331 autoAnnMenu.add(showConsensusHistogram);
2332 autoAnnMenu.add(showSequenceLogo);
2333 autoAnnMenu.add(normaliseSequenceLogo);
2334 autoAnnMenu.addSeparator();
2335 autoAnnMenu.add(showGroupConservation);
2336 autoAnnMenu.add(showGroupConsensus);
2337 annotationsMenu.add(autoAnnMenu);
2338 viewMenu.addSeparator();
2339 viewMenu.add(showSeqFeatures);
2340 // viewMenu.add(showSeqFeaturesHeight);
2342 viewMenu.add(openFeatureSettings);
2343 tooltipSettingsMenu.add(showDbRefsMenuitem);
2344 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2345 viewMenu.add(tooltipSettingsMenu);
2346 viewMenu.addSeparator();
2347 viewMenu.add(alignmentProperties);
2348 viewMenu.addSeparator();
2349 viewMenu.add(overviewMenuItem);
2350 colourMenu.add(applyToAllGroups);
2351 colourMenu.add(textColour);
2352 colourMenu.addSeparator();
2353 colourMenu.add(noColourmenuItem);
2354 colourMenu.add(clustalColour);
2355 colourMenu.add(BLOSUM62Colour);
2356 colourMenu.add(PIDColour);
2357 colourMenu.add(zappoColour);
2358 colourMenu.add(taylorColour);
2359 colourMenu.add(hydrophobicityColour);
2360 colourMenu.add(helixColour);
2361 colourMenu.add(strandColour);
2362 colourMenu.add(turnColour);
2363 colourMenu.add(buriedColour);
2364 colourMenu.add(nucleotideColour);
2365 colourMenu.add(purinePyrimidineColour);
2366 colourMenu.add(RNAInteractionColour);
2367 // colourMenu.add(covariationColour);
2368 colourMenu.add(tcoffeeColour);
2369 colourMenu.add(userDefinedColour);
2370 colourMenu.addSeparator();
2371 colourMenu.add(conservationMenuItem);
2372 colourMenu.add(modifyConservation);
2373 colourMenu.add(abovePIDThreshold);
2374 colourMenu.add(modifyPID);
2375 colourMenu.add(annotationColour);
2376 colourMenu.add(rnahelicesColour);
2377 calculateMenu.add(sort);
2378 calculateMenu.add(calculateTree);
2379 calculateMenu.addSeparator();
2380 calculateMenu.add(pairwiseAlignmentMenuItem);
2381 calculateMenu.add(PCAMenuItem);
2382 calculateMenu.addSeparator();
2383 calculateMenu.add(showTranslation);
2384 calculateMenu.add(cdna);
2385 calculateMenu.add(showProducts);
2386 calculateMenu.add(autoCalculate);
2387 calculateMenu.add(sortByTree);
2388 calculateMenu.addSeparator();
2389 calculateMenu.add(extractScores);
2390 webServiceNoServices = new JMenuItem(
2391 MessageManager.getString("label.no_services"));
2392 webService.add(webServiceNoServices);
2393 pasteMenu.add(pasteNew);
2394 pasteMenu.add(pasteThis);
2395 sort.add(sortIDMenuItem);
2396 sort.add(sortLengthMenuItem);
2397 sort.add(sortGroupMenuItem);
2398 sort.add(sortPairwiseMenuItem);
2399 sort.add(sortByTreeMenu);
2400 jMenu2.add(htmlMenuItem);
2401 jMenu2.add(epsFile);
2402 jMenu2.add(createPNG);
2403 jMenu2.add(createSVG);
2404 addSequenceMenu.add(addFromFile);
2405 addSequenceMenu.add(addFromText);
2406 addSequenceMenu.add(addFromURL);
2407 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2408 statusPanel.add(statusBar, null);
2409 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2410 jMenu3.add(showAllColumns);
2411 jMenu3.add(showAllSeqs);
2412 jMenu3.add(showAllhidden);
2413 hideMenu.add(hideSelColumns);
2414 hideMenu.add(hideSelSequences);
2415 hideMenu.add(hideAllSelection);
2416 hideMenu.add(hideAllButSelection);
2418 formatMenu.add(font);
2419 formatMenu.addSeparator();
2420 formatMenu.add(wrapMenuItem);
2421 formatMenu.add(scaleAbove);
2422 formatMenu.add(scaleLeft);
2423 formatMenu.add(scaleRight);
2424 formatMenu.add(seqLimits);
2425 formatMenu.add(idRightAlign);
2426 formatMenu.add(hiddenMarkers);
2427 formatMenu.add(viewBoxesMenuItem);
2428 formatMenu.add(viewTextMenuItem);
2429 formatMenu.add(colourTextMenuItem);
2430 formatMenu.add(renderGapsMenuItem);
2431 formatMenu.add(centreColumnLabelsMenuItem);
2432 formatMenu.add(showNonconservedMenuItem);
2433 selectMenu.add(findMenuItem);
2434 selectMenu.addSeparator();
2435 selectMenu.add(selectAllSequenceMenuItem);
2436 selectMenu.add(deselectAllSequenceMenuItem);
2437 selectMenu.add(invertSequenceMenuItem);
2438 selectMenu.add(invertColSel);
2439 selectMenu.add(createGroup);
2440 selectMenu.add(unGroup);
2441 selectMenu.add(grpsFromSelection);
2442 selectMenu.add(deleteGroups);
2443 calculateMenu.add(expandAlignment);
2444 // TODO - determine if the listenToViewSelections button is needed : see bug
2446 // selectMenu.addSeparator();
2447 // selectMenu.add(listenToViewSelections);
2450 protected void viewAsCdna_actionPerformed()
2454 protected void alignCdna_actionPerformed()
2458 protected void linkCdna_actionPerformed()
2463 * Action on clicking sort annotations by type.
2467 protected void sortAnnotations_actionPerformed()
2472 * Action on clicking Show all annotations.
2474 * @param forSequences
2475 * update sequence-related annotations
2476 * @param forAlignment
2477 * update non-sequence-related annotations
2479 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2480 boolean forAlignment)
2482 setAnnotationsVisibility(true, forSequences, forAlignment);
2486 * Action on clicking Hide all annotations.
2488 * @param forSequences
2489 * update sequence-related annotations
2490 * @param forAlignment
2491 * update non-sequence-related annotations
2493 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2494 boolean forAlignment)
2496 setAnnotationsVisibility(false, forSequences, forAlignment);
2500 * Set the visibility of annotations to true or false. Can act on
2501 * sequence-related annotations, or alignment-related, or both.
2504 * @param forSequences
2505 * update sequence-related annotations
2506 * @param forAlignment
2507 * update non-sequence-related annotations
2509 protected void setAnnotationsVisibility(boolean visible,
2510 boolean forSequences, boolean forAlignment)
2515 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2517 // TODO Auto-generated method stub
2521 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2523 // TODO Auto-generated method stub
2527 protected void showAllhidden_actionPerformed(ActionEvent e)
2529 // TODO Auto-generated method stub
2533 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2535 // TODO Auto-generated method stub
2539 protected void hideAllSelection_actionPerformed(ActionEvent e)
2541 // TODO Auto-generated method stub
2545 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2547 // TODO Auto-generated method stub
2551 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2553 // TODO Auto-generated method stub
2557 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2559 // TODO Auto-generated method stub
2563 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2565 // TODO Auto-generated method stub
2569 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2571 // TODO Auto-generated method stub
2575 protected void showGroupConservation_actionPerformed(ActionEvent e)
2577 // TODO Auto-generated method stub
2581 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2583 // TODO Auto-generated method stub
2587 protected void showSeqFeaturesHeight_actionPerformed(
2588 ActionEvent actionEvent)
2590 // TODO Auto-generated method stub
2594 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2596 // TODO Auto-generated method stub
2600 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2602 // TODO Auto-generated method stub
2606 protected void followHighlight_actionPerformed()
2608 // TODO Auto-generated method stub
2612 protected void showNpFeats_actionPerformed(ActionEvent e)
2614 // TODO Auto-generated method stub
2618 protected void showDbRefs_actionPerformed(ActionEvent e)
2620 // TODO Auto-generated method stub
2624 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2628 protected void buildSortByAnnotationScoresMenu()
2632 protected void extractScores_actionPerformed(ActionEvent e)
2636 protected void outputText_actionPerformed(ActionEvent e)
2640 public void addFromFile_actionPerformed(ActionEvent e)
2645 public void addFromText_actionPerformed(ActionEvent e)
2650 public void addFromURL_actionPerformed(ActionEvent e)
2655 public void exportFeatures_actionPerformed(ActionEvent e)
2660 public void exportAnnotations_actionPerformed(ActionEvent e)
2665 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2669 protected void closeMenuItem_actionPerformed(boolean b)
2673 protected void redoMenuItem_actionPerformed(ActionEvent e)
2677 protected void undoMenuItem_actionPerformed(ActionEvent e)
2681 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2685 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2689 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2693 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2697 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2701 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2705 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2709 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2713 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2717 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2721 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2725 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2729 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2733 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2737 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2741 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2745 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2749 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2753 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2757 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2761 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2765 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2769 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2773 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2777 protected void clustalColour_actionPerformed(ActionEvent e)
2781 protected void zappoColour_actionPerformed(ActionEvent e)
2785 protected void taylorColour_actionPerformed(ActionEvent e)
2789 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2793 protected void helixColour_actionPerformed(ActionEvent e)
2797 protected void strandColour_actionPerformed(ActionEvent e)
2801 protected void turnColour_actionPerformed(ActionEvent e)
2805 protected void buriedColour_actionPerformed(ActionEvent e)
2809 protected void userDefinedColour_actionPerformed(ActionEvent e)
2813 protected void PIDColour_actionPerformed(ActionEvent e)
2817 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2821 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2825 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2830 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2833 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2837 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2841 protected void printMenuItem_actionPerformed(ActionEvent e)
2845 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2849 protected void findMenuItem_actionPerformed(ActionEvent e)
2853 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2857 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2861 protected void nucleotideColour_actionPerformed(ActionEvent e)
2865 protected void deleteGroups_actionPerformed(ActionEvent e)
2869 protected void createGroup_actionPerformed(ActionEvent e)
2873 protected void unGroup_actionPerformed(ActionEvent e)
2877 protected void copy_actionPerformed(ActionEvent e)
2881 protected void cut_actionPerformed(ActionEvent e)
2885 protected void delete_actionPerformed(ActionEvent e)
2889 protected void pasteNew_actionPerformed(ActionEvent e)
2893 protected void pasteThis_actionPerformed(ActionEvent e)
2897 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2901 public void createPNG(java.io.File f)
2905 protected void font_actionPerformed(ActionEvent e)
2909 protected void seqLimit_actionPerformed(ActionEvent e)
2913 public void seqDBRef_actionPerformed(ActionEvent e)
2918 public void createEPS(java.io.File f)
2922 public void createSVG(java.io.File f)
2926 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2932 * Template method to handle the 'load T-Coffee scores' menu event.
2934 * Subclasses override this method to provide a custom action.
2939 protected void loadScores_actionPerformed(ActionEvent event)
2945 * Template method to handle the 'Color T-Coffee scores' menu event.
2947 * Subclasses override this method to provide a custom action.
2952 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2957 protected void jpred_actionPerformed(ActionEvent e)
2961 protected void scaleAbove_actionPerformed(ActionEvent e)
2965 protected void scaleLeft_actionPerformed(ActionEvent e)
2969 protected void scaleRight_actionPerformed(ActionEvent e)
2973 protected void modifyPID_actionPerformed(ActionEvent e)
2977 protected void modifyConservation_actionPerformed(ActionEvent e)
2981 protected void saveAs_actionPerformed(ActionEvent e)
2985 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2989 public void vamsasStore_actionPerformed(ActionEvent e)
2994 public void vamsasLoad_actionPerformed(ActionEvent e)
2999 public void showTranslation_actionPerformed(ActionEvent e)
3004 public void featureSettings_actionPerformed(ActionEvent e)
3009 public void fetchSequence_actionPerformed(ActionEvent e)
3014 public void smoothFont_actionPerformed(ActionEvent e)
3019 public void annotationColour_actionPerformed(ActionEvent e)
3024 public void rnahelicesColour_actionPerformed(ActionEvent e)
3029 public void associatedData_actionPerformed(ActionEvent e)
3034 public void autoCalculate_actionPerformed(ActionEvent e)
3039 public void sortByTreeOption_actionPerformed(ActionEvent e)
3044 public void showAllSeqs_actionPerformed(ActionEvent e)
3049 public void showAllColumns_actionPerformed(ActionEvent e)
3054 public void hideSelSequences_actionPerformed(ActionEvent e)
3059 public void hideSelColumns_actionPerformed(ActionEvent e)
3064 public void hiddenMarkers_actionPerformed(ActionEvent e)
3069 public void findPdbId_actionPerformed(ActionEvent e)
3074 public void enterPdbId_actionPerformed(ActionEvent e)
3079 public void pdbFile_actionPerformed(ActionEvent e)
3084 public void invertColSel_actionPerformed(ActionEvent e)
3089 public void tabSelectionChanged(int sel)
3094 public void tabbedPane_mousePressed(MouseEvent e)
3099 public void tabbedPane_focusGained(FocusEvent e)
3104 public void save_actionPerformed(ActionEvent e)
3109 public void reload_actionPerformed(ActionEvent e)
3114 public void newView_actionPerformed(ActionEvent e)
3119 public void textColour_actionPerformed(ActionEvent e)
3124 public void idRightAlign_actionPerformed(ActionEvent e)
3129 public void expandViews_actionPerformed(ActionEvent e)
3134 public void gatherViews_actionPerformed(ActionEvent e)
3139 public void buildTreeMenu()
3144 public void pageSetup_actionPerformed(ActionEvent e)
3149 public void alignmentProperties()
3154 protected void expand_newalign(ActionEvent e)
3156 // TODO Auto-generated method stub
3160 protected boolean isShowAutoCalculatedAbove()
3162 return showAutoCalculatedAbove;
3165 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3167 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3170 protected SequenceAnnotationOrder getAnnotationSortOrder()
3172 return annotationSortOrder;
3175 protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3177 this.annotationSortOrder = annotationSortOrder;