JAL-1372 i18n and tweaking set/unset representative sequence
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3  * Copyright (C) 2014 The Jalview Authors
4  * 
5  * This file is part of Jalview.
6  * 
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.
11  *  
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.
16  * 
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.
20  */
21 package jalview.jbgui;
22
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;
29
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;
40
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;
57
58 public class GAlignFrame extends JInternalFrame
59 {
60   protected JMenuBar alignFrameMenuBar = new JMenuBar();
61
62   protected JMenu fileMenu = new JMenu();
63
64   protected JMenuItem closeMenuItem = new JMenuItem();
65
66   protected JMenu editMenu = new JMenu();
67
68   protected JMenu viewMenu = new JMenu();
69
70   protected JMenu annotationsMenu = new JMenu();
71
72   protected JMenu colourMenu = new JMenu();
73
74   protected JMenu calculateMenu = new JMenu();
75
76   protected JMenu webService = new JMenu();
77
78   protected JMenuItem webServiceNoServices;
79
80   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
81
82   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
83
84   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
85
86   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
87
88   protected JMenuItem remove2RightMenuItem = new JMenuItem();
89
90   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
91
92   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
93
94   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
95
96   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
97
98   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
99
100   protected JMenuItem sortIDMenuItem = new JMenuItem();
101
102   protected JMenuItem sortLengthMenuItem = new JMenuItem();
103
104   protected JMenuItem sortGroupMenuItem = new JMenuItem();
105
106   protected JMenu sortByAnnotScore = new JMenu();
107
108   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
109
110   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
111
112   protected JMenuItem PCAMenuItem = new JMenuItem();
113
114   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
115
116   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
117
118   BorderLayout borderLayout1 = new BorderLayout();
119
120   public JLabel statusBar = new JLabel();
121
122   protected JMenuItem saveAs = new JMenuItem();
123
124   protected JMenu outputTextboxMenu = new JMenu();
125
126   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
127
128   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
129
130   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
131
132   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
133
134   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
135
136   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
137
138   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
139
140   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
141
142   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
143
144   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
145
146   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
147
148   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
149
150   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
151
152   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
153
154   // protected JRadioButtonMenuItem covariationColour = new
155   // JRadioButtonMenuItem();
156
157   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
158
159   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
160
161   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
162
163   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
164
165   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
166
167   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
168
169   JMenuItem htmlMenuItem = new JMenuItem();
170
171   JMenuItem overviewMenuItem = new JMenuItem();
172
173   protected JMenuItem undoMenuItem = new JMenuItem();
174
175   protected JMenuItem redoMenuItem = new JMenuItem();
176
177   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
178
179   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
180
181   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
182
183   JMenuItem printMenuItem = new JMenuItem();
184
185   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
186
187   JMenuItem findMenuItem = new JMenuItem();
188
189   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
190
191   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
192
193   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
194
195   JMenuItem deleteGroups = new JMenuItem();
196
197   JMenuItem createGroup = new JMenuItem();
198
199   JMenuItem unGroup = new JMenuItem();
200
201   JMenuItem delete = new JMenuItem();
202
203   JMenuItem copy = new JMenuItem();
204
205   JMenuItem cut = new JMenuItem();
206
207   JMenu pasteMenu = new JMenu();
208
209   JMenuItem pasteNew = new JMenuItem();
210
211   JMenuItem pasteThis = new JMenuItem();
212
213   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
214
215   JMenuItem createPNG = new JMenuItem();
216
217   JMenuItem createBioJS = new JMenuItem();
218
219   JMenuItem createSVG = new JMenuItem();
220
221   protected JMenuItem font = new JMenuItem();
222
223   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
224
225   JMenuItem epsFile = new JMenuItem();
226
227   JMenuItem LoadtreeMenuItem = new JMenuItem();
228
229   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
230
231   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
232
233   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
234
235   protected JMenuItem modifyPID = new JMenuItem();
236
237   protected JMenuItem modifyConservation = new JMenuItem();
238
239   protected JMenu sortByTreeMenu = new JMenu();
240
241   protected JMenu sort = new JMenu();
242
243   protected JMenu calculateTree = new JMenu();
244
245   JMenu jMenu2 = new JMenu();
246
247   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
248
249   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
250
251   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
252
253   protected ButtonGroup colours = new ButtonGroup();
254
255   JMenuItem vamsasStore = new JMenuItem();
256
257   protected JMenuItem showTranslation = new JMenuItem();
258
259   protected JMenuItem extractScores = new JMenuItem();
260
261   protected JMenuItem expandAlignment = new JMenuItem();
262
263   protected JMenu showProducts = new JMenu();
264
265   public JMenuItem openFeatureSettings = new JMenuItem();
266
267   JMenuItem fetchSequence = new JMenuItem();
268
269   JMenuItem annotationColour = new JMenuItem();
270
271   protected JMenuItem rnahelicesColour = new JMenuItem();
272
273   JMenuItem associatedData = new JMenuItem();
274
275   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
276
277   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
278
279   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
280
281   JMenu addSequenceMenu = new JMenu();
282
283   JMenuItem addFromFile = new JMenuItem();
284
285   JMenuItem addFromText = new JMenuItem();
286
287   JMenuItem addFromURL = new JMenuItem();
288
289   JMenuItem exportAnnotations = new JMenuItem();
290
291   JMenuItem exportFeatures = new JMenuItem();
292
293   protected JPanel statusPanel = new JPanel();
294
295   GridLayout gridLayout1 = new GridLayout();
296
297   JMenu jMenu3 = new JMenu();
298
299   JMenuItem showAllSeqs = new JMenuItem();
300
301   JMenuItem showAllColumns = new JMenuItem();
302
303   JMenu hideMenu = new JMenu();
304
305   JMenuItem hideSelSequences = new JMenuItem();
306
307   JMenuItem hideSelColumns = new JMenuItem();
308
309   JMenuItem hideAllButSelection = new JMenuItem();
310
311   JMenuItem hideAllSelection = new JMenuItem();
312
313   JMenuItem showAllhidden = new JMenuItem();
314
315   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
316
317   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
318
319   protected JMenuItem showAllAlAnnotations = new JMenuItem();
320
321   protected JMenuItem hideAllAlAnnotations = new JMenuItem();
322
323   protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
324
325   protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
326
327   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
328
329   JMenuItem invertColSel = new JMenuItem();
330
331   protected JTabbedPane tabbedPane = new JTabbedPane();
332
333   JMenuItem save = new JMenuItem();
334
335   protected JMenuItem reload = new JMenuItem();
336
337   JMenuItem newView = new JMenuItem();
338
339   JMenuItem textColour = new JMenuItem();
340
341   JMenu formatMenu = new JMenu();
342
343   JMenu selectMenu = new JMenu();
344
345   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
346
347   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
348
349   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
350
351   protected JMenuItem gatherViews = new JMenuItem();
352
353   protected JMenuItem expandViews = new JMenuItem();
354
355   JMenuItem pageSetup = new JMenuItem();
356
357   JMenuItem alignmentProperties = new JMenuItem();
358
359   JMenu tooltipSettingsMenu = new JMenu();
360
361   private JMenuItem justifyLeftMenuItem = new JMenuItem();
362
363   private JMenuItem justifyRightMenuItem = new JMenuItem();
364
365   JMenu autoAnnMenu = new JMenu();
366
367   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
368
369   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
370
371   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
372
373   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
374
375   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
376
377   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
378
379   protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
380
381   protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
382
383   private JMenuItem grpsFromSelection = new JMenuItem();
384
385   private SequenceAnnotationOrder annotationSortOrder;
386
387   private boolean showAutoCalculatedAbove = false;
388
389   public GAlignFrame()
390   {
391     try
392     {
393       jbInit();
394       setJMenuBar(alignFrameMenuBar);
395
396       // dynamically fill save as menu with available formats
397       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
398       {
399         JMenuItem item = new JMenuItem(
400                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
401
402         item.addActionListener(new java.awt.event.ActionListener()
403         {
404           @Override
405           public void actionPerformed(ActionEvent e)
406           {
407             outputText_actionPerformed(e);
408           }
409         });
410
411         outputTextboxMenu.add(item);
412       }
413     } catch (Exception e)
414     {
415       System.err.println(e.toString());
416     }
417
418     if (!new jalview.util.Platform().isAMac())
419     {
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');
428     }
429
430     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
431     {
432       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
433               .getUserColourSchemes().keys();
434
435       while (userColours.hasMoreElements())
436       {
437         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
438                 userColours.nextElement().toString());
439         radioItem.setName("USER_DEFINED");
440         radioItem.addMouseListener(new MouseAdapter()
441         {
442           @Override
443           public void mousePressed(MouseEvent evt)
444           {
445             if (evt.isControlDown()
446                     || SwingUtilities.isRightMouseButton(evt))
447             {
448               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
449
450               int option = JOptionPane.showInternalConfirmDialog(
451                       jalview.gui.Desktop.desktop,
452                       MessageManager
453                               .getString("label.remove_from_default_list"),
454                       MessageManager
455                               .getString("label.remove_user_defined_colour"),
456                       JOptionPane.YES_NO_OPTION);
457               if (option == JOptionPane.YES_OPTION)
458               {
459                 jalview.gui.UserDefinedColours
460                         .removeColourFromDefaults(radioItem.getText());
461                 colourMenu.remove(radioItem);
462               }
463               else
464               {
465                 radioItem.addActionListener(new ActionListener()
466                 {
467                   @Override
468                   public void actionPerformed(ActionEvent evt)
469                   {
470                     userDefinedColour_actionPerformed(evt);
471                   }
472                 });
473               }
474             }
475           }
476         });
477         radioItem.addActionListener(new ActionListener()
478         {
479           @Override
480           public void actionPerformed(ActionEvent evt)
481           {
482             userDefinedColour_actionPerformed(evt);
483           }
484         });
485         colourMenu.insert(radioItem, 15);
486         colours.add(radioItem);
487       }
488     }
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"));
508
509   }
510
511   public void setColourSelected(String defaultColour)
512   {
513
514     if (defaultColour != null)
515     {
516       int index = ColourSchemeProperty
517               .getColourIndexFromName(defaultColour);
518
519       switch (index)
520       {
521       case ColourSchemeProperty.CLUSTAL:
522         clustalColour.setSelected(true);
523
524         break;
525
526       case ColourSchemeProperty.BLOSUM:
527         BLOSUM62Colour.setSelected(true);
528
529         break;
530
531       case ColourSchemeProperty.PID:
532         PIDColour.setSelected(true);
533
534         break;
535
536       case ColourSchemeProperty.ZAPPO:
537         zappoColour.setSelected(true);
538
539         break;
540
541       case ColourSchemeProperty.TAYLOR:
542         taylorColour.setSelected(true);
543         break;
544
545       case ColourSchemeProperty.HYDROPHOBIC:
546         hydrophobicityColour.setSelected(true);
547
548         break;
549
550       case ColourSchemeProperty.HELIX:
551         helixColour.setSelected(true);
552
553         break;
554
555       case ColourSchemeProperty.STRAND:
556         strandColour.setSelected(true);
557
558         break;
559
560       case ColourSchemeProperty.TURN:
561         turnColour.setSelected(true);
562
563         break;
564
565       case ColourSchemeProperty.BURIED:
566         buriedColour.setSelected(true);
567
568         break;
569
570       case ColourSchemeProperty.NUCLEOTIDE:
571         nucleotideColour.setSelected(true);
572
573         break;
574
575       case ColourSchemeProperty.TCOFFEE:
576         tcoffeeColour.setSelected(true);
577         break;
578
579       case ColourSchemeProperty.PURINEPYRIMIDINE:
580         purinePyrimidineColour.setSelected(true);
581
582         break;
583
584       case ColourSchemeProperty.RNAINTERACTION:
585         RNAInteractionColour.setSelected(true);
586
587         break;
588       /*
589        * case ColourSchemeProperty.COVARIATION:
590        * covariationColour.setSelected(true);
591        * 
592        * break;
593        */
594       case ColourSchemeProperty.USER_DEFINED:
595         userDefinedColour.setSelected(true);
596
597         break;
598       case ColourSchemeProperty.NONE:
599       default:
600         noColourmenuItem.setSelected(true);
601         break;
602
603       }
604     }
605
606   }
607
608   private void jbInit() throws Exception
609   {
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()
617     {
618       @Override
619       public void actionPerformed(ActionEvent e)
620       {
621         saveAs_actionPerformed(e);
622       }
623     });
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()
629     {
630       @Override
631       public void actionPerformed(ActionEvent e)
632       {
633         closeMenuItem_actionPerformed(false);
634       }
635     });
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()
649             {
650               @Override
651               public void actionPerformed(ActionEvent e)
652               {
653                 selectAllSequenceMenuItem_actionPerformed(e);
654               }
655             });
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()
662             {
663               @Override
664               public void actionPerformed(ActionEvent e)
665               {
666                 deselectAllSequenceMenuItem_actionPerformed(e);
667               }
668             });
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()
676             {
677               @Override
678               public void actionPerformed(ActionEvent e)
679               {
680                 invertSequenceMenuItem_actionPerformed(e);
681               }
682             });
683     grpsFromSelection.setText(MessageManager
684             .getString("action.make_groups_selection"));
685     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
686     {
687       @Override
688       public void actionPerformed(ActionEvent e)
689       {
690         makeGrpsFromSelection_actionPerformed(e);
691       }
692     });
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()
698     {
699       @Override
700       public void actionPerformed(ActionEvent e)
701       {
702         expand_newalign(e);
703       }
704     });
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));
710     remove2LeftMenuItem
711             .addActionListener(new java.awt.event.ActionListener()
712             {
713               @Override
714               public void actionPerformed(ActionEvent e)
715               {
716                 remove2LeftMenuItem_actionPerformed(e);
717               }
718             });
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));
724     remove2RightMenuItem
725             .addActionListener(new java.awt.event.ActionListener()
726             {
727               @Override
728               public void actionPerformed(ActionEvent e)
729               {
730                 remove2RightMenuItem_actionPerformed(e);
731               }
732             });
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()
740             {
741               @Override
742               public void actionPerformed(ActionEvent e)
743               {
744                 removeGappedColumnMenuItem_actionPerformed(e);
745               }
746             });
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()
755             {
756               @Override
757               public void actionPerformed(ActionEvent e)
758               {
759                 removeAllGapsMenuItem_actionPerformed(e);
760               }
761             });
762     justifyLeftMenuItem.setText(MessageManager
763             .getString("action.left_justify_alignment"));
764     justifyLeftMenuItem
765             .addActionListener(new java.awt.event.ActionListener()
766             {
767               @Override
768               public void actionPerformed(ActionEvent e)
769               {
770                 justifyLeftMenuItem_actionPerformed(e);
771               }
772             });
773     justifyRightMenuItem.setText(MessageManager
774             .getString("action.right_justify_alignment"));
775     justifyRightMenuItem
776             .addActionListener(new java.awt.event.ActionListener()
777             {
778               @Override
779               public void actionPerformed(ActionEvent e)
780               {
781                 justifyRightMenuItem_actionPerformed(e);
782               }
783             });
784     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
785     viewBoxesMenuItem.setState(true);
786     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
787     {
788       @Override
789       public void actionPerformed(ActionEvent e)
790       {
791         viewBoxesMenuItem_actionPerformed(e);
792       }
793     });
794     viewTextMenuItem.setText(MessageManager.getString("action.text"));
795     viewTextMenuItem.setState(true);
796     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
797     {
798       @Override
799       public void actionPerformed(ActionEvent e)
800       {
801         viewTextMenuItem_actionPerformed(e);
802       }
803     });
804     showNonconservedMenuItem.setText(MessageManager
805             .getString("label.show_non_conversed"));
806     showNonconservedMenuItem.setState(false);
807     showNonconservedMenuItem
808             .addActionListener(new java.awt.event.ActionListener()
809             {
810               @Override
811               public void actionPerformed(ActionEvent e)
812               {
813                 showUnconservedMenuItem_actionPerformed(e);
814               }
815             });
816     sortPairwiseMenuItem.setText(MessageManager
817             .getString("action.by_pairwise_id"));
818     sortPairwiseMenuItem
819             .addActionListener(new java.awt.event.ActionListener()
820             {
821               @Override
822               public void actionPerformed(ActionEvent e)
823               {
824                 sortPairwiseMenuItem_actionPerformed(e);
825               }
826             });
827     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
828     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
829     {
830       @Override
831       public void actionPerformed(ActionEvent e)
832       {
833         sortIDMenuItem_actionPerformed(e);
834       }
835     });
836     sortLengthMenuItem
837             .setText(MessageManager.getString("action.by_length"));
838     sortLengthMenuItem
839             .addActionListener(new java.awt.event.ActionListener()
840             {
841               @Override
842               public void actionPerformed(ActionEvent e)
843               {
844                 sortLengthMenuItem_actionPerformed(e);
845               }
846             });
847     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
848     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
849     {
850       @Override
851       public void actionPerformed(ActionEvent e)
852       {
853         sortGroupMenuItem_actionPerformed(e);
854       }
855     });
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()
863             {
864               @Override
865               public void actionPerformed(ActionEvent e)
866               {
867                 removeRedundancyMenuItem_actionPerformed(e);
868               }
869             });
870     pairwiseAlignmentMenuItem.setText(MessageManager
871             .getString("action.pairwise_alignment"));
872     pairwiseAlignmentMenuItem
873             .addActionListener(new java.awt.event.ActionListener()
874             {
875               @Override
876               public void actionPerformed(ActionEvent e)
877               {
878                 pairwiseAlignmentMenuItem_actionPerformed(e);
879               }
880             });
881     PCAMenuItem.setText(MessageManager
882             .getString("label.principal_component_analysis"));
883     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
884     {
885       @Override
886       public void actionPerformed(ActionEvent e)
887       {
888         PCAMenuItem_actionPerformed(e);
889       }
890     });
891     averageDistanceTreeMenuItem.setText(MessageManager
892             .getString("label.average_distance_identity"));
893     averageDistanceTreeMenuItem
894             .addActionListener(new java.awt.event.ActionListener()
895             {
896               @Override
897               public void actionPerformed(ActionEvent e)
898               {
899                 averageDistanceTreeMenuItem_actionPerformed(e);
900               }
901             });
902     neighbourTreeMenuItem.setText(MessageManager
903             .getString("label.neighbour_joining_identity"));
904     neighbourTreeMenuItem
905             .addActionListener(new java.awt.event.ActionListener()
906             {
907               @Override
908               public void actionPerformed(ActionEvent e)
909               {
910                 neighbourTreeMenuItem_actionPerformed(e);
911               }
912             });
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"));
922
923     clustalColour.addActionListener(new java.awt.event.ActionListener()
924     {
925       @Override
926       public void actionPerformed(ActionEvent e)
927       {
928         clustalColour_actionPerformed(e);
929       }
930     });
931     zappoColour.setText(MessageManager.getString("label.zappo"));
932     zappoColour.addActionListener(new java.awt.event.ActionListener()
933     {
934       @Override
935       public void actionPerformed(ActionEvent e)
936       {
937         zappoColour_actionPerformed(e);
938       }
939     });
940     taylorColour.setText(MessageManager.getString("label.taylor"));
941     taylorColour.addActionListener(new java.awt.event.ActionListener()
942     {
943       @Override
944       public void actionPerformed(ActionEvent e)
945       {
946         taylorColour_actionPerformed(e);
947       }
948     });
949     hydrophobicityColour.setText(MessageManager
950             .getString("label.hydrophobicity"));
951     hydrophobicityColour
952             .addActionListener(new java.awt.event.ActionListener()
953             {
954               @Override
955               public void actionPerformed(ActionEvent e)
956               {
957                 hydrophobicityColour_actionPerformed(e);
958               }
959             });
960     helixColour.setText(MessageManager.getString("label.helix_propensity"));
961     helixColour.addActionListener(new java.awt.event.ActionListener()
962     {
963       @Override
964       public void actionPerformed(ActionEvent e)
965       {
966         helixColour_actionPerformed(e);
967       }
968     });
969     strandColour.setText(MessageManager
970             .getString("label.strand_propensity"));
971     strandColour.addActionListener(new java.awt.event.ActionListener()
972     {
973       @Override
974       public void actionPerformed(ActionEvent e)
975       {
976         strandColour_actionPerformed(e);
977       }
978     });
979     turnColour.setText(MessageManager.getString("label.turn_propensity"));
980     turnColour.addActionListener(new java.awt.event.ActionListener()
981     {
982       @Override
983       public void actionPerformed(ActionEvent e)
984       {
985         turnColour_actionPerformed(e);
986       }
987     });
988     buriedColour.setText(MessageManager.getString("label.buried_index"));
989     buriedColour.addActionListener(new java.awt.event.ActionListener()
990     {
991       @Override
992       public void actionPerformed(ActionEvent e)
993       {
994         buriedColour_actionPerformed(e);
995       }
996     });
997     userDefinedColour.setText(MessageManager
998             .getString("action.user_defined"));
999     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1000     {
1001       @Override
1002       public void actionPerformed(ActionEvent e)
1003       {
1004         userDefinedColour_actionPerformed(e);
1005       }
1006     });
1007     PIDColour
1008             .setText(MessageManager.getString("label.percentage_identity"));
1009     PIDColour.addActionListener(new java.awt.event.ActionListener()
1010     {
1011       @Override
1012       public void actionPerformed(ActionEvent e)
1013       {
1014         PIDColour_actionPerformed(e);
1015       }
1016     });
1017     BLOSUM62Colour
1018             .setText(MessageManager.getString("label.blosum62_score"));
1019     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1020     {
1021       @Override
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         BLOSUM62Colour_actionPerformed(e);
1025       }
1026     });
1027     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1028     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1029     {
1030       @Override
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         nucleotideColour_actionPerformed(e);
1034       }
1035     });
1036
1037     purinePyrimidineColour.setText(MessageManager
1038             .getString("label.purine_pyrimidine"));
1039     purinePyrimidineColour
1040             .addActionListener(new java.awt.event.ActionListener()
1041             {
1042               @Override
1043               public void actionPerformed(ActionEvent e)
1044               {
1045                 purinePyrimidineColour_actionPerformed(e);
1046               }
1047             });
1048
1049     RNAInteractionColour.setText("RNA Interaction type");
1050     RNAInteractionColour
1051             .addActionListener(new java.awt.event.ActionListener()
1052             {
1053               @Override
1054               public void actionPerformed(ActionEvent e)
1055               {
1056                 RNAInteractionColour_actionPerformed(e);
1057               }
1058             });
1059     /*
1060      * covariationColour.setText("Covariation");
1061      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1062      * public void actionPerformed(ActionEvent e) {
1063      * covariationColour_actionPerformed(e); } });
1064      */
1065
1066     avDistanceTreeBlosumMenuItem.setText(MessageManager
1067             .getString("label.average_distance_bloslum62"));
1068     avDistanceTreeBlosumMenuItem
1069             .addActionListener(new java.awt.event.ActionListener()
1070             {
1071               @Override
1072               public void actionPerformed(ActionEvent e)
1073               {
1074                 avTreeBlosumMenuItem_actionPerformed(e);
1075               }
1076             });
1077     njTreeBlosumMenuItem.setText(MessageManager
1078             .getString("label.neighbour_blosum62"));
1079     njTreeBlosumMenuItem
1080             .addActionListener(new java.awt.event.ActionListener()
1081             {
1082               @Override
1083               public void actionPerformed(ActionEvent e)
1084               {
1085                 njTreeBlosumMenuItem_actionPerformed(e);
1086               }
1087             });
1088     annotationPanelMenuItem.setActionCommand("");
1089     annotationPanelMenuItem.setText(MessageManager
1090             .getString("label.show_annotations"));
1091     annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1092             true));
1093     annotationPanelMenuItem.addActionListener(new ActionListener()
1094     {
1095       @Override
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         annotationPanelMenuItem_actionPerformed(e);
1099       }
1100     });
1101     showAllAlAnnotations.setText(MessageManager
1102             .getString("label.show_all_al_annotations"));
1103     final boolean isAnnotationPanelShown = annotationPanelMenuItem
1104             .getState();
1105     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1106     showAllAlAnnotations.addActionListener(new ActionListener()
1107     {
1108       @Override
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         showAllAnnotations_actionPerformed(false, true);
1112       }
1113     });
1114     hideAllAlAnnotations.setText(MessageManager
1115             .getString("label.hide_all_al_annotations"));
1116     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1117     hideAllAlAnnotations.addActionListener(new ActionListener()
1118     {
1119       @Override
1120       public void actionPerformed(ActionEvent e)
1121       {
1122         hideAllAnnotations_actionPerformed(false, true);
1123       }
1124     });
1125     showAllSeqAnnotations.setText(MessageManager
1126             .getString("label.show_all_seq_annotations"));
1127     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1128     showAllSeqAnnotations.addActionListener(new ActionListener()
1129     {
1130       @Override
1131       public void actionPerformed(ActionEvent e)
1132       {
1133         showAllAnnotations_actionPerformed(true, false);
1134       }
1135     });
1136     hideAllSeqAnnotations.setText(MessageManager
1137             .getString("label.hide_all_seq_annotations"));
1138     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1139     hideAllSeqAnnotations.addActionListener(new ActionListener()
1140     {
1141       @Override
1142       public void actionPerformed(ActionEvent e)
1143       {
1144         hideAllAnnotations_actionPerformed(true, false);
1145       }
1146     });
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"));
1152     sortAnnBySequence
1153             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1154     sortAnnBySequence.addActionListener(new ActionListener()
1155     {
1156       @Override
1157       public void actionPerformed(ActionEvent e)
1158       {
1159         boolean newState = sortAnnBySequence.getState();
1160         sortAnnByLabel.setSelected(false);
1161         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1162                 : SequenceAnnotationOrder.NONE);
1163         sortAnnotations_actionPerformed();
1164       }
1165     });
1166     sortAnnByLabel.setText(MessageManager
1167             .getString("label.sort_annotations_by_label"));
1168     sortAnnByLabel
1169             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1170     sortAnnByLabel.addActionListener(new ActionListener()
1171     {
1172       @Override
1173       public void actionPerformed(ActionEvent e)
1174       {
1175         boolean newState = sortAnnByLabel.getState();
1176         sortAnnBySequence.setSelected(false);
1177         setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1178                 : SequenceAnnotationOrder.NONE);
1179         sortAnnotations_actionPerformed();
1180       }
1181     });
1182     colourTextMenuItem.setText(MessageManager
1183             .getString("label.colour_text"));
1184     colourTextMenuItem
1185             .addActionListener(new java.awt.event.ActionListener()
1186             {
1187               @Override
1188               public void actionPerformed(ActionEvent e)
1189               {
1190                 colourTextMenuItem_actionPerformed(e);
1191               }
1192             });
1193     htmlMenuItem.setText(MessageManager.getString("label.html"));
1194     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1195     {
1196       @Override
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         htmlMenuItem_actionPerformed(e);
1200       }
1201     });
1202
1203     // TODO uncomment when supported by MassageManager
1204     // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
1205     createBioJS.setText("BioJS");
1206     createBioJS.addActionListener(new java.awt.event.ActionListener()
1207     {
1208       @Override
1209       public void actionPerformed(ActionEvent e)
1210       {
1211         bioJSMenuItem_actionPerformed(e);
1212       }
1213     });
1214
1215     overviewMenuItem.setText(MessageManager
1216             .getString("label.overview_window"));
1217     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1218     {
1219       @Override
1220       public void actionPerformed(ActionEvent e)
1221       {
1222         overviewMenuItem_actionPerformed(e);
1223       }
1224     });
1225     undoMenuItem.setEnabled(false);
1226     undoMenuItem.setText(MessageManager.getString("action.undo"));
1227     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1228             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1229                     .getMenuShortcutKeyMask(), false));
1230     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1231     {
1232       @Override
1233       public void actionPerformed(ActionEvent e)
1234       {
1235         undoMenuItem_actionPerformed(e);
1236       }
1237     });
1238     redoMenuItem.setEnabled(false);
1239     redoMenuItem.setText(MessageManager.getString("action.redo"));
1240     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1241             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1242                     .getMenuShortcutKeyMask(), false));
1243     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1244     {
1245       @Override
1246       public void actionPerformed(ActionEvent e)
1247       {
1248         redoMenuItem_actionPerformed(e);
1249       }
1250     });
1251     conservationMenuItem.setText(MessageManager
1252             .getString("action.by_conservation"));
1253     conservationMenuItem
1254             .addActionListener(new java.awt.event.ActionListener()
1255             {
1256               @Override
1257               public void actionPerformed(ActionEvent e)
1258               {
1259                 conservationMenuItem_actionPerformed(e);
1260               }
1261             });
1262     noColourmenuItem.setText(MessageManager.getString("label.none"));
1263     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1264     {
1265       @Override
1266       public void actionPerformed(ActionEvent e)
1267       {
1268         noColourmenuItem_actionPerformed(e);
1269       }
1270     });
1271     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1272     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1273     {
1274       @Override
1275       public void actionPerformed(ActionEvent e)
1276       {
1277         wrapMenuItem_actionPerformed(e);
1278       }
1279     });
1280     printMenuItem.setText(MessageManager.getString("action.print") + "...");
1281     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1282             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1283                     .getMenuShortcutKeyMask(), false));
1284     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1285     {
1286       @Override
1287       public void actionPerformed(ActionEvent e)
1288       {
1289         printMenuItem_actionPerformed(e);
1290       }
1291     });
1292     renderGapsMenuItem
1293             .setText(MessageManager.getString("action.show_gaps"));
1294     renderGapsMenuItem.setState(true);
1295     renderGapsMenuItem
1296             .addActionListener(new java.awt.event.ActionListener()
1297             {
1298               @Override
1299               public void actionPerformed(ActionEvent e)
1300               {
1301                 renderGapsMenuItem_actionPerformed(e);
1302               }
1303             });
1304     findMenuItem.setText(MessageManager.getString("action.find"));
1305     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1306             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1307                     .getMenuShortcutKeyMask(), false));
1308     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1309             MessageManager.getString("label.find_tip")));
1310     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1311     {
1312       @Override
1313       public void actionPerformed(ActionEvent e)
1314       {
1315         findMenuItem_actionPerformed(e);
1316       }
1317     });
1318     abovePIDThreshold.setText(MessageManager
1319             .getString("label.above_identity_threshold"));
1320     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1321     {
1322       @Override
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         abovePIDThreshold_actionPerformed(e);
1326       }
1327     });
1328     showSeqFeatures.setText(MessageManager
1329             .getString("label.show_sequence_features"));
1330     showSeqFeatures.addActionListener(new ActionListener()
1331     {
1332       @Override
1333       public void actionPerformed(ActionEvent actionEvent)
1334       {
1335         showSeqFeatures_actionPerformed(actionEvent);
1336       }
1337     });
1338     /*
1339      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1340      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1341      * void actionPerformed(ActionEvent actionEvent) {
1342      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1343      */
1344     showDbRefsMenuitem.setText(MessageManager
1345             .getString("label.show_database_refs"));
1346     showDbRefsMenuitem.addActionListener(new ActionListener()
1347     {
1348
1349       @Override
1350       public void actionPerformed(ActionEvent e)
1351       {
1352         showDbRefs_actionPerformed(e);
1353       }
1354
1355     });
1356     showNpFeatsMenuitem.setText(MessageManager
1357             .getString("label.show_non_positional_features"));
1358     showNpFeatsMenuitem.addActionListener(new ActionListener()
1359     {
1360
1361       @Override
1362       public void actionPerformed(ActionEvent e)
1363       {
1364         showNpFeats_actionPerformed(e);
1365       }
1366
1367     });
1368     showGroupConservation.setText(MessageManager
1369             .getString("label.group_conservation"));
1370     showGroupConservation.addActionListener(new ActionListener()
1371     {
1372
1373       @Override
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         showGroupConservation_actionPerformed(e);
1377       }
1378
1379     });
1380
1381     showGroupConsensus.setText(MessageManager
1382             .getString("label.group_consensus"));
1383     showGroupConsensus.addActionListener(new ActionListener()
1384     {
1385
1386       @Override
1387       public void actionPerformed(ActionEvent e)
1388       {
1389         showGroupConsensus_actionPerformed(e);
1390       }
1391
1392     });
1393     showConsensusHistogram.setText(MessageManager
1394             .getString("label.show_consensus_histogram"));
1395     showConsensusHistogram.addActionListener(new ActionListener()
1396     {
1397
1398       @Override
1399       public void actionPerformed(ActionEvent e)
1400       {
1401         showConsensusHistogram_actionPerformed(e);
1402       }
1403
1404     });
1405     showSequenceLogo.setText(MessageManager
1406             .getString("label.show_consensus_logo"));
1407     showSequenceLogo.addActionListener(new ActionListener()
1408     {
1409
1410       @Override
1411       public void actionPerformed(ActionEvent e)
1412       {
1413         showSequenceLogo_actionPerformed(e);
1414       }
1415
1416     });
1417     normaliseSequenceLogo.setText(MessageManager
1418             .getString("label.norm_consensus_logo"));
1419     normaliseSequenceLogo.addActionListener(new ActionListener()
1420     {
1421
1422       @Override
1423       public void actionPerformed(ActionEvent e)
1424       {
1425         normaliseSequenceLogo_actionPerformed(e);
1426       }
1427
1428     });
1429     applyAutoAnnotationSettings.setText(MessageManager
1430             .getString("label.apply_all_groups"));
1431     applyAutoAnnotationSettings.setState(false);
1432     applyAutoAnnotationSettings.setVisible(true);
1433     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1434     {
1435       @Override
1436       public void actionPerformed(ActionEvent e)
1437       {
1438         applyAutoAnnotationSettings_actionPerformed(e);
1439       }
1440     });
1441
1442     ButtonGroup buttonGroup = new ButtonGroup();
1443     buttonGroup.add(showAutoFirst);
1444     buttonGroup.add(showAutoLast);
1445     showAutoFirst.setText(MessageManager.getString("label.show_first"));
1446     showAutoFirst.setSelected(Cache.getDefault(
1447             Preferences.SHOW_AUTOCALC_ABOVE,
1448             false));
1449     showAutoFirst.addActionListener(new ActionListener()
1450     {
1451       @Override
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1455         sortAnnotations_actionPerformed();
1456       }
1457     });
1458     showAutoLast.setText(MessageManager.getString("label.show_last"));
1459     showAutoLast.setSelected(!showAutoFirst.isSelected());
1460     showAutoLast.addActionListener(new ActionListener()
1461     {
1462       @Override
1463       public void actionPerformed(ActionEvent e)
1464       {
1465         setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1466         sortAnnotations_actionPerformed();
1467       }
1468     });
1469
1470     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1471     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1472     {
1473       @Override
1474       public void actionPerformed(ActionEvent e)
1475       {
1476         nucleotideColour_actionPerformed(e);
1477       }
1478     });
1479
1480     tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1481     tcoffeeColour.setEnabled(false);
1482     tcoffeeColour.addActionListener(new ActionListener()
1483     {
1484
1485       @Override
1486       public void actionPerformed(ActionEvent e)
1487       {
1488         tcoffeeColorScheme_actionPerformed(e);
1489       }
1490     });
1491
1492     deleteGroups
1493             .setText(MessageManager.getString("action.undefine_groups"));
1494     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1495             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1496                     .getMenuShortcutKeyMask(), false));
1497     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1498     {
1499       @Override
1500       public void actionPerformed(ActionEvent e)
1501       {
1502         deleteGroups_actionPerformed(e);
1503       }
1504     });
1505     createGroup.setText(MessageManager.getString("action.create_groups"));
1506     createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1507             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1508                     .getMenuShortcutKeyMask(), false));
1509     createGroup.addActionListener(new java.awt.event.ActionListener()
1510     {
1511       @Override
1512       public void actionPerformed(ActionEvent e)
1513       {
1514         createGroup_actionPerformed(e);
1515       }
1516     });
1517     unGroup.setText(MessageManager.getString("action.remove_group"));
1518     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1519             java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1520                     .getMenuShortcutKeyMask()
1521                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1522     unGroup.addActionListener(new java.awt.event.ActionListener()
1523     {
1524       @Override
1525       public void actionPerformed(ActionEvent e)
1526       {
1527         unGroup_actionPerformed(e);
1528       }
1529     });
1530     copy.setText(MessageManager.getString("action.copy"));
1531     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1532             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1533                     .getMenuShortcutKeyMask(), false));
1534
1535     copy.addActionListener(new java.awt.event.ActionListener()
1536     {
1537       @Override
1538       public void actionPerformed(ActionEvent e)
1539       {
1540         copy_actionPerformed(e);
1541       }
1542     });
1543     cut.setText(MessageManager.getString("action.cut"));
1544     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1545             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1546                     .getMenuShortcutKeyMask(), false));
1547     cut.addActionListener(new java.awt.event.ActionListener()
1548     {
1549       @Override
1550       public void actionPerformed(ActionEvent e)
1551       {
1552         cut_actionPerformed(e);
1553       }
1554     });
1555     delete.setText(MessageManager.getString("action.delete"));
1556     delete.addActionListener(new java.awt.event.ActionListener()
1557     {
1558       @Override
1559       public void actionPerformed(ActionEvent e)
1560       {
1561         delete_actionPerformed(e);
1562       }
1563     });
1564     pasteMenu.setText(MessageManager.getString("action.paste"));
1565     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1566     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1567             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1568                     .getMenuShortcutKeyMask()
1569                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1570     pasteNew.addActionListener(new java.awt.event.ActionListener()
1571     {
1572       @Override
1573       public void actionPerformed(ActionEvent e)
1574       {
1575         pasteNew_actionPerformed(e);
1576       }
1577     });
1578     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1579     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1580             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1581                     .getMenuShortcutKeyMask(), false));
1582     pasteThis.addActionListener(new java.awt.event.ActionListener()
1583     {
1584       @Override
1585       public void actionPerformed(ActionEvent e)
1586       {
1587         pasteThis_actionPerformed(e);
1588       }
1589     });
1590     applyToAllGroups.setText(MessageManager
1591             .getString("label.apply_colour_to_all_groups"));
1592     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1593     {
1594       @Override
1595       public void actionPerformed(ActionEvent e)
1596       {
1597         applyToAllGroups_actionPerformed(e);
1598       }
1599     });
1600     createPNG.addActionListener(new java.awt.event.ActionListener()
1601     {
1602       @Override
1603       public void actionPerformed(ActionEvent e)
1604       {
1605         createPNG(null);
1606       }
1607     });
1608     createPNG.setActionCommand(MessageManager
1609             .getString("label.save_png_image"));
1610     createPNG.setText("PNG");
1611
1612     font.setText(MessageManager.getString("action.font"));
1613     font.addActionListener(new java.awt.event.ActionListener()
1614     {
1615       @Override
1616       public void actionPerformed(ActionEvent e)
1617       {
1618         font_actionPerformed(e);
1619       }
1620     });
1621     seqLimits.setText(MessageManager
1622             .getString("label.show_sequence_limits"));
1623     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1624     seqLimits.addActionListener(new java.awt.event.ActionListener()
1625     {
1626       @Override
1627       public void actionPerformed(ActionEvent e)
1628       {
1629         seqLimit_actionPerformed(e);
1630       }
1631     });
1632     epsFile.setText("EPS");
1633     epsFile.addActionListener(new java.awt.event.ActionListener()
1634     {
1635       @Override
1636       public void actionPerformed(ActionEvent e)
1637       {
1638         createEPS(null);
1639       }
1640     });
1641
1642     createSVG.setText("SVG");
1643     createSVG.addActionListener(new java.awt.event.ActionListener()
1644     {
1645       @Override
1646       public void actionPerformed(ActionEvent e)
1647       {
1648         createSVG(null);
1649       }
1650     });
1651
1652     LoadtreeMenuItem.setActionCommand(MessageManager
1653             .getString("label.load_tree_for_sequence_set"));
1654     LoadtreeMenuItem.setText(MessageManager
1655             .getString("label.load_associated_tree"));
1656     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1657     {
1658       @Override
1659       public void actionPerformed(ActionEvent e)
1660       {
1661         LoadtreeMenuItem_actionPerformed(e);
1662       }
1663     });
1664
1665     scaleAbove.setVisible(false);
1666     scaleAbove.setText(MessageManager.getString("action.scale_above"));
1667     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1668     {
1669       @Override
1670       public void actionPerformed(ActionEvent e)
1671       {
1672         scaleAbove_actionPerformed(e);
1673       }
1674     });
1675     scaleLeft.setVisible(false);
1676     scaleLeft.setSelected(true);
1677     scaleLeft.setText(MessageManager.getString("action.scale_left"));
1678     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1679     {
1680       @Override
1681       public void actionPerformed(ActionEvent e)
1682       {
1683         scaleLeft_actionPerformed(e);
1684       }
1685     });
1686     scaleRight.setVisible(false);
1687     scaleRight.setSelected(true);
1688     scaleRight.setText(MessageManager.getString("action.scale_right"));
1689     scaleRight.addActionListener(new java.awt.event.ActionListener()
1690     {
1691       @Override
1692       public void actionPerformed(ActionEvent e)
1693       {
1694         scaleRight_actionPerformed(e);
1695       }
1696     });
1697     centreColumnLabelsMenuItem.setVisible(true);
1698     centreColumnLabelsMenuItem.setState(false);
1699     centreColumnLabelsMenuItem.setText(MessageManager
1700             .getString("label.centre_column_labels"));
1701     centreColumnLabelsMenuItem
1702             .addActionListener(new java.awt.event.ActionListener()
1703             {
1704               @Override
1705               public void actionPerformed(ActionEvent e)
1706               {
1707                 centreColumnLabels_actionPerformed(e);
1708               }
1709             });
1710     followHighlightMenuItem.setVisible(true);
1711     followHighlightMenuItem.setState(true);
1712     followHighlightMenuItem.setText(MessageManager
1713             .getString("label.automatic_scrolling"));
1714     followHighlightMenuItem.addActionListener(new ActionListener()
1715     {
1716
1717       @Override
1718       public void actionPerformed(ActionEvent e)
1719       {
1720         followHighlight_actionPerformed();
1721       }
1722
1723     });
1724
1725     modifyPID.setText(MessageManager
1726             .getString("label.modify_identity_thereshold"));
1727     modifyPID.addActionListener(new java.awt.event.ActionListener()
1728     {
1729       @Override
1730       public void actionPerformed(ActionEvent e)
1731       {
1732         modifyPID_actionPerformed(e);
1733       }
1734     });
1735     modifyConservation.setText(MessageManager
1736             .getString("label.modify_conservation_thereshold"));
1737     modifyConservation
1738             .addActionListener(new java.awt.event.ActionListener()
1739             {
1740               @Override
1741               public void actionPerformed(ActionEvent e)
1742               {
1743                 modifyConservation_actionPerformed(e);
1744               }
1745             });
1746     sortByTreeMenu
1747             .setText(MessageManager.getString("action.by_tree_order"));
1748     sort.setText(MessageManager.getString("action.sort"));
1749     sort.addMenuListener(new MenuListener()
1750     {
1751       @Override
1752       public void menuSelected(MenuEvent e)
1753       {
1754         buildTreeMenu();
1755       }
1756
1757       @Override
1758       public void menuDeselected(MenuEvent e)
1759       {
1760       }
1761
1762       @Override
1763       public void menuCanceled(MenuEvent e)
1764       {
1765       }
1766     });
1767     sortByAnnotScore.setText(MessageManager
1768             .getString("label.sort_by_score"));
1769     sort.add(sortByAnnotScore);
1770     sort.addMenuListener(new javax.swing.event.MenuListener()
1771     {
1772
1773       @Override
1774       public void menuCanceled(MenuEvent e)
1775       {
1776       }
1777
1778       @Override
1779       public void menuDeselected(MenuEvent e)
1780       {
1781       }
1782
1783       @Override
1784       public void menuSelected(MenuEvent e)
1785       {
1786         buildSortByAnnotationScoresMenu();
1787       }
1788     });
1789     sortByAnnotScore.setVisible(false);
1790
1791     calculateTree
1792             .setText(MessageManager.getString("action.calculate_tree"));
1793
1794     jMenu2.setText(MessageManager.getString("label.export_image"));
1795     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1796     padGapsMenuitem.setState(jalview.bin.Cache
1797             .getDefault("PAD_GAPS", false));
1798     padGapsMenuitem.addActionListener(new ActionListener()
1799     {
1800       @Override
1801       public void actionPerformed(ActionEvent e)
1802       {
1803         padGapsMenuitem_actionPerformed(e);
1804       }
1805     });
1806     vamsasStore.setVisible(false);
1807     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1808     vamsasStore.addActionListener(new ActionListener()
1809     {
1810       @Override
1811       public void actionPerformed(ActionEvent e)
1812       {
1813         vamsasStore_actionPerformed(e);
1814       }
1815     });
1816     showTranslation.setText(MessageManager
1817             .getString("label.translate_cDNA"));
1818     showTranslation.addActionListener(new ActionListener()
1819     {
1820       @Override
1821       public void actionPerformed(ActionEvent e)
1822       {
1823         showTranslation_actionPerformed(e);
1824       }
1825     });
1826     extractScores.setText(MessageManager.getString("label.extract_scores")
1827             + "...");
1828     extractScores.addActionListener(new ActionListener()
1829     {
1830       @Override
1831       public void actionPerformed(ActionEvent e)
1832       {
1833         extractScores_actionPerformed(e);
1834       }
1835     });
1836     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1837     // score extraction
1838     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1839     /*
1840      * showProducts.addActionListener(new ActionListener() {
1841      * 
1842      * public void actionPerformed(ActionEvent e) {
1843      * showProducts_actionPerformed(e); } });
1844      */
1845     openFeatureSettings.setText(MessageManager
1846             .getString("label.feature_settings"));
1847     openFeatureSettings.addActionListener(new ActionListener()
1848     {
1849       @Override
1850       public void actionPerformed(ActionEvent e)
1851       {
1852         featureSettings_actionPerformed(e);
1853       }
1854     });
1855     fetchSequence
1856             .setText(MessageManager.getString("label.fetch_sequences"));
1857     fetchSequence.addActionListener(new ActionListener()
1858     {
1859       @Override
1860       public void actionPerformed(ActionEvent e)
1861       {
1862         fetchSequence_actionPerformed(e);
1863       }
1864     });
1865
1866     annotationColour.setText(MessageManager
1867             .getString("action.by_annotation"));
1868     annotationColour.addActionListener(new ActionListener()
1869     {
1870       @Override
1871       public void actionPerformed(ActionEvent e)
1872       {
1873         annotationColour_actionPerformed(e);
1874       }
1875     });
1876
1877     rnahelicesColour.setText(MessageManager
1878             .getString("action.by_rna_helixes"));
1879     rnahelicesColour.addActionListener(new ActionListener()
1880     {
1881       @Override
1882       public void actionPerformed(ActionEvent e)
1883       {
1884         rnahelicesColour_actionPerformed(e);
1885       }
1886     });
1887
1888     associatedData.setText(MessageManager
1889             .getString("label.load_features_annotations"));
1890     associatedData.addActionListener(new ActionListener()
1891     {
1892       @Override
1893       public void actionPerformed(ActionEvent e)
1894       {
1895         associatedData_actionPerformed(e);
1896       }
1897     });
1898     autoCalculate.setText(MessageManager
1899             .getString("label.autocalculate_consensus"));
1900     autoCalculate.setState(jalview.bin.Cache.getDefault(
1901             "AUTO_CALC_CONSENSUS", true));
1902     autoCalculate.addActionListener(new ActionListener()
1903     {
1904       @Override
1905       public void actionPerformed(ActionEvent e)
1906       {
1907         autoCalculate_actionPerformed(e);
1908       }
1909     });
1910     sortByTree.setText(MessageManager
1911             .getString("label.sort_alignment_new_tree"));
1912     sortByTree
1913             .setToolTipText("<html>"
1914                     + MessageManager
1915                             .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1916     sortByTree
1917             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1918     sortByTree.addActionListener(new ActionListener()
1919     {
1920       @Override
1921       public void actionPerformed(ActionEvent e)
1922       {
1923         sortByTreeOption_actionPerformed(e);
1924       }
1925     });
1926
1927     listenToViewSelections.setText(MessageManager
1928             .getString("label.listen_for_selections"));
1929     listenToViewSelections
1930             .setToolTipText("<html>"
1931                     + MessageManager
1932                             .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1933     listenToViewSelections.setState(false);
1934     listenToViewSelections.addActionListener(new ActionListener()
1935     {
1936       @Override
1937       public void actionPerformed(ActionEvent e)
1938       {
1939         listenToViewSelections_actionPerformed(e);
1940       }
1941     });
1942
1943     addSequenceMenu
1944             .setText(MessageManager.getString("label.add_sequences"));
1945     addFromFile.setText(MessageManager.getString("label.from_file"));
1946     addFromFile.addActionListener(new ActionListener()
1947     {
1948       @Override
1949       public void actionPerformed(ActionEvent e)
1950       {
1951         addFromFile_actionPerformed(e);
1952       }
1953     });
1954     addFromText.setText(MessageManager.getString("label.from_textbox"));
1955     addFromText.addActionListener(new ActionListener()
1956     {
1957       @Override
1958       public void actionPerformed(ActionEvent e)
1959       {
1960         addFromText_actionPerformed(e);
1961       }
1962     });
1963     addFromURL.setText(MessageManager.getString("label.from_url"));
1964     addFromURL.addActionListener(new ActionListener()
1965     {
1966       @Override
1967       public void actionPerformed(ActionEvent e)
1968       {
1969         addFromURL_actionPerformed(e);
1970       }
1971     });
1972     exportFeatures.setText(MessageManager
1973             .getString("label.export_features"));
1974     exportFeatures.addActionListener(new ActionListener()
1975     {
1976       @Override
1977       public void actionPerformed(ActionEvent e)
1978       {
1979         exportFeatures_actionPerformed(e);
1980       }
1981     });
1982     exportAnnotations.setText(MessageManager
1983             .getString("label.export_annotations"));
1984     exportAnnotations.addActionListener(new ActionListener()
1985     {
1986       @Override
1987       public void actionPerformed(ActionEvent e)
1988       {
1989         exportAnnotations_actionPerformed(e);
1990       }
1991     });
1992     statusPanel.setLayout(gridLayout1);
1993     jMenu3.setText(MessageManager.getString("action.show"));
1994     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1995     showAllSeqs.setToolTipText(MessageManager
1996             .getString("label.toggle_sequence_visibility"));
1997     showAllSeqs.addActionListener(new ActionListener()
1998     {
1999       @Override
2000       public void actionPerformed(ActionEvent e)
2001       {
2002         showAllSeqs_actionPerformed(e);
2003       }
2004     });
2005     showAllColumns.setText(MessageManager.getString("label.all_columns"));
2006     showAllColumns.setToolTipText(MessageManager
2007             .getString("label.toggle_columns_visibility"));
2008     showAllColumns.addActionListener(new ActionListener()
2009     {
2010       @Override
2011       public void actionPerformed(ActionEvent e)
2012       {
2013         showAllColumns_actionPerformed(e);
2014       }
2015     });
2016     hideMenu.setText(MessageManager.getString("action.hide"));
2017     hideSelSequences.setText(MessageManager
2018             .getString("label.selected_sequences"));
2019     hideSelSequences.setToolTipText(MessageManager
2020             .getString("label.toggle_sequence_visibility"));
2021     hideSelSequences.addActionListener(new ActionListener()
2022     {
2023       @Override
2024       public void actionPerformed(ActionEvent e)
2025       {
2026         hideSelSequences_actionPerformed(e);
2027       }
2028     });
2029     hideSelColumns.setText(MessageManager
2030             .getString("label.selected_columns"));
2031     hideSelColumns.setToolTipText(MessageManager
2032             .getString("label.toggle_columns_visibility"));
2033     hideSelColumns.addActionListener(new ActionListener()
2034     {
2035       @Override
2036       public void actionPerformed(ActionEvent e)
2037       {
2038         hideSelColumns_actionPerformed(e);
2039       }
2040     });
2041     hideAllSelection.setText(MessageManager
2042             .getString("label.selected_region"));
2043     hideAllSelection.addActionListener(new ActionListener()
2044     {
2045       @Override
2046       public void actionPerformed(ActionEvent e)
2047       {
2048         hideAllSelection_actionPerformed(e);
2049       }
2050     });
2051     // TODO: should be hidden if no selection exists.
2052     hideAllButSelection.setText(MessageManager
2053             .getString("label.all_but_selected_region"));
2054     hideAllButSelection.addActionListener(new ActionListener()
2055     {
2056       @Override
2057       public void actionPerformed(ActionEvent e)
2058       {
2059         hideAllButSelection_actionPerformed(e);
2060       }
2061     });
2062     showAllhidden.setText(MessageManager
2063             .getString("label.all_sequences_columns"));
2064     showAllhidden.setToolTipText(MessageManager
2065             .getString("label.toggles_visibility_hidden_selected_regions"));
2066     showAllhidden.addActionListener(new ActionListener()
2067     {
2068       @Override
2069       public void actionPerformed(ActionEvent e)
2070       {
2071         showAllhidden_actionPerformed(e);
2072       }
2073     });
2074     hiddenMarkers.setText(MessageManager
2075             .getString("action.show_hidden_markers"));
2076     hiddenMarkers.addActionListener(new ActionListener()
2077     {
2078       @Override
2079       public void actionPerformed(ActionEvent e)
2080       {
2081         hiddenMarkers_actionPerformed(e);
2082       }
2083     });
2084     invertColSel.setText(MessageManager
2085             .getString("action.invert_column_selection"));
2086     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2087             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2088                     .getMenuShortcutKeyMask()
2089                     | java.awt.event.KeyEvent.ALT_MASK, false));
2090     invertColSel.addActionListener(new ActionListener()
2091     {
2092       @Override
2093       public void actionPerformed(ActionEvent e)
2094       {
2095         invertColSel_actionPerformed(e);
2096       }
2097     });
2098     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2099     {
2100       @Override
2101       public void stateChanged(ChangeEvent evt)
2102       {
2103         JTabbedPane pane = (JTabbedPane) evt.getSource();
2104         int sel = pane.getSelectedIndex();
2105         tabSelectionChanged(sel);
2106       }
2107     });
2108     tabbedPane.addMouseListener(new MouseAdapter()
2109     {
2110       @Override
2111       public void mousePressed(MouseEvent e)
2112       {
2113         tabbedPane_mousePressed(e);
2114       }
2115     });
2116     tabbedPane.addFocusListener(new FocusAdapter()
2117     {
2118       @Override
2119       public void focusGained(FocusEvent e)
2120       {
2121         tabbedPane_focusGained(e);
2122       }
2123     });
2124     save.setText(MessageManager.getString("action.save"));
2125     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2126             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2127                     .getMenuShortcutKeyMask(), false));
2128     save.addActionListener(new ActionListener()
2129     {
2130       @Override
2131       public void actionPerformed(ActionEvent e)
2132       {
2133         save_actionPerformed(e);
2134       }
2135     });
2136     reload.setEnabled(false);
2137     reload.setText(MessageManager.getString("action.reload"));
2138     reload.addActionListener(new ActionListener()
2139     {
2140       @Override
2141       public void actionPerformed(ActionEvent e)
2142       {
2143         reload_actionPerformed(e);
2144       }
2145     });
2146     newView.setText(MessageManager.getString("action.new_view"));
2147     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2148             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2149                     .getMenuShortcutKeyMask(), false));
2150     newView.addActionListener(new ActionListener()
2151     {
2152       @Override
2153       public void actionPerformed(ActionEvent e)
2154       {
2155         newView_actionPerformed(e);
2156       }
2157     });
2158     tabbedPane.setToolTipText("<html><i>"
2159             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2160             + "</i></html>");
2161     textColour.setText(MessageManager.getString("label.colour_text")
2162             + "...");
2163     textColour.addActionListener(new ActionListener()
2164     {
2165       @Override
2166       public void actionPerformed(ActionEvent e)
2167       {
2168         textColour_actionPerformed(e);
2169       }
2170     });
2171     formatMenu.setText(MessageManager.getString("action.format"));
2172     selectMenu.setText(MessageManager.getString("action.select"));
2173     idRightAlign.setText(MessageManager
2174             .getString("label.right_align_sequence_id"));
2175     idRightAlign.addActionListener(new ActionListener()
2176     {
2177       @Override
2178       public void actionPerformed(ActionEvent e)
2179       {
2180         idRightAlign_actionPerformed(e);
2181       }
2182     });
2183     gatherViews.setEnabled(false);
2184     gatherViews.setText(MessageManager.getString("action.gather_views"));
2185     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2186             java.awt.event.KeyEvent.VK_G, 0, false));
2187     gatherViews.addActionListener(new ActionListener()
2188     {
2189       @Override
2190       public void actionPerformed(ActionEvent e)
2191       {
2192         gatherViews_actionPerformed(e);
2193       }
2194     });
2195     expandViews.setEnabled(false);
2196     expandViews.setText(MessageManager.getString("action.expand_views"));
2197     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2198             java.awt.event.KeyEvent.VK_X, 0, false));
2199     expandViews.addActionListener(new ActionListener()
2200     {
2201       @Override
2202       public void actionPerformed(ActionEvent e)
2203       {
2204         expandViews_actionPerformed(e);
2205       }
2206     });
2207     pageSetup
2208             .setText(MessageManager.getString("action.page_setup") + "...");
2209     pageSetup.addActionListener(new ActionListener()
2210     {
2211       @Override
2212       public void actionPerformed(ActionEvent e)
2213       {
2214         pageSetup_actionPerformed(e);
2215       }
2216     });
2217     alignmentProperties.setText(MessageManager
2218             .getString("label.alignment_props") + "...");
2219     alignmentProperties.addActionListener(new ActionListener()
2220     {
2221       @Override
2222       public void actionPerformed(ActionEvent actionEvent)
2223       {
2224         alignmentProperties();
2225       }
2226     });
2227     tooltipSettingsMenu.setText(MessageManager
2228             .getString("label.sequence_id_tooltip"));
2229     autoAnnMenu.setText(MessageManager
2230             .getString("label.autocalculated_annotation"));
2231     alignFrameMenuBar.add(fileMenu);
2232     alignFrameMenuBar.add(editMenu);
2233     alignFrameMenuBar.add(selectMenu);
2234     alignFrameMenuBar.add(viewMenu);
2235     alignFrameMenuBar.add(annotationsMenu);
2236     alignFrameMenuBar.add(formatMenu);
2237     alignFrameMenuBar.add(colourMenu);
2238     alignFrameMenuBar.add(calculateMenu);
2239     alignFrameMenuBar.add(webService);
2240     fileMenu.add(fetchSequence);
2241     fileMenu.add(addSequenceMenu);
2242     fileMenu.add(reload);
2243     fileMenu.addSeparator();
2244     fileMenu.add(vamsasStore);
2245     fileMenu.add(save);
2246     fileMenu.add(saveAs);
2247     fileMenu.add(outputTextboxMenu);
2248     fileMenu.add(pageSetup);
2249     fileMenu.add(printMenuItem);
2250     fileMenu.addSeparator();
2251     fileMenu.add(jMenu2);
2252     fileMenu.add(exportFeatures);
2253     fileMenu.add(exportAnnotations);
2254     fileMenu.add(LoadtreeMenuItem);
2255     fileMenu.add(associatedData);
2256     fileMenu.addSeparator();
2257     fileMenu.add(closeMenuItem);
2258     editMenu.add(undoMenuItem);
2259     editMenu.add(redoMenuItem);
2260     editMenu.add(cut);
2261     editMenu.add(copy);
2262     editMenu.add(pasteMenu);
2263     editMenu.add(delete);
2264     editMenu.addSeparator();
2265     editMenu.add(remove2LeftMenuItem);
2266     editMenu.add(remove2RightMenuItem);
2267     editMenu.add(removeGappedColumnMenuItem);
2268     editMenu.add(removeAllGapsMenuItem);
2269     editMenu.add(removeRedundancyMenuItem);
2270     editMenu.addSeparator();
2271     // dont add these yet in the CVS build - they cannot be undone!
2272     // Excluded from Jalview 2.5 release - undo needs to be implemented.
2273     // editMenu.add(justifyLeftMenuItem);
2274     // editMenu.add(justifyRightMenuItem);
2275     // editMenu.addSeparator();
2276     editMenu.add(padGapsMenuitem);
2277     viewMenu.add(newView);
2278     viewMenu.add(expandViews);
2279     viewMenu.add(gatherViews);
2280     viewMenu.addSeparator();
2281     viewMenu.add(jMenu3);
2282     viewMenu.add(hideMenu);
2283     viewMenu.addSeparator();
2284     viewMenu.add(followHighlightMenuItem);
2285     annotationsMenu.add(annotationPanelMenuItem);
2286     annotationsMenu.addSeparator();
2287     annotationsMenu.add(showAllAlAnnotations);
2288     annotationsMenu.add(hideAllAlAnnotations);
2289     annotationsMenu.addSeparator();
2290     annotationsMenu.add(showAllSeqAnnotations);
2291     annotationsMenu.add(hideAllSeqAnnotations);
2292     annotationsMenu.add(sortAnnBySequence);
2293     annotationsMenu.add(sortAnnByLabel);
2294     annotationsMenu.addSeparator();
2295     autoAnnMenu.add(showAutoFirst);
2296     autoAnnMenu.add(showAutoLast);
2297     autoAnnMenu.addSeparator();
2298     autoAnnMenu.add(applyAutoAnnotationSettings);
2299     autoAnnMenu.add(showConsensusHistogram);
2300     autoAnnMenu.add(showSequenceLogo);
2301     autoAnnMenu.add(normaliseSequenceLogo);
2302     autoAnnMenu.addSeparator();
2303     autoAnnMenu.add(showGroupConservation);
2304     autoAnnMenu.add(showGroupConsensus);
2305     annotationsMenu.add(autoAnnMenu);
2306     viewMenu.addSeparator();
2307     viewMenu.add(showSeqFeatures);
2308     // viewMenu.add(showSeqFeaturesHeight);
2309
2310     viewMenu.add(openFeatureSettings);
2311     tooltipSettingsMenu.add(showDbRefsMenuitem);
2312     tooltipSettingsMenu.add(showNpFeatsMenuitem);
2313     viewMenu.add(tooltipSettingsMenu);
2314     viewMenu.addSeparator();
2315     viewMenu.add(alignmentProperties);
2316     viewMenu.addSeparator();
2317     viewMenu.add(overviewMenuItem);
2318     colourMenu.add(applyToAllGroups);
2319     colourMenu.add(textColour);
2320     colourMenu.addSeparator();
2321     colourMenu.add(noColourmenuItem);
2322     colourMenu.add(clustalColour);
2323     colourMenu.add(BLOSUM62Colour);
2324     colourMenu.add(PIDColour);
2325     colourMenu.add(zappoColour);
2326     colourMenu.add(taylorColour);
2327     colourMenu.add(hydrophobicityColour);
2328     colourMenu.add(helixColour);
2329     colourMenu.add(strandColour);
2330     colourMenu.add(turnColour);
2331     colourMenu.add(buriedColour);
2332     colourMenu.add(nucleotideColour);
2333     colourMenu.add(purinePyrimidineColour);
2334     colourMenu.add(RNAInteractionColour);
2335     // colourMenu.add(covariationColour);
2336     colourMenu.add(tcoffeeColour);
2337     colourMenu.add(userDefinedColour);
2338     colourMenu.addSeparator();
2339     colourMenu.add(conservationMenuItem);
2340     colourMenu.add(modifyConservation);
2341     colourMenu.add(abovePIDThreshold);
2342     colourMenu.add(modifyPID);
2343     colourMenu.add(annotationColour);
2344     colourMenu.add(rnahelicesColour);
2345     calculateMenu.add(sort);
2346     calculateMenu.add(calculateTree);
2347     calculateMenu.addSeparator();
2348     calculateMenu.add(pairwiseAlignmentMenuItem);
2349     calculateMenu.add(PCAMenuItem);
2350     calculateMenu.addSeparator();
2351     calculateMenu.add(showTranslation);
2352     calculateMenu.add(showProducts);
2353     calculateMenu.add(autoCalculate);
2354     calculateMenu.add(sortByTree);
2355     calculateMenu.addSeparator();
2356     calculateMenu.add(extractScores);
2357     webServiceNoServices = new JMenuItem(
2358             MessageManager.getString("label.no_services"));
2359     webService.add(webServiceNoServices);
2360     pasteMenu.add(pasteNew);
2361     pasteMenu.add(pasteThis);
2362     sort.add(sortIDMenuItem);
2363     sort.add(sortLengthMenuItem);
2364     sort.add(sortGroupMenuItem);
2365     sort.add(sortPairwiseMenuItem);
2366     sort.add(sortByTreeMenu);
2367     jMenu2.add(htmlMenuItem);
2368     jMenu2.add(epsFile);
2369     jMenu2.add(createPNG);
2370     jMenu2.add(createBioJS);
2371     jMenu2.add(createSVG);
2372     addSequenceMenu.add(addFromFile);
2373     addSequenceMenu.add(addFromText);
2374     addSequenceMenu.add(addFromURL);
2375     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2376     statusPanel.add(statusBar, null);
2377     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2378     jMenu3.add(showAllColumns);
2379     jMenu3.add(showAllSeqs);
2380     jMenu3.add(showAllhidden);
2381     hideMenu.add(hideSelColumns);
2382     hideMenu.add(hideSelSequences);
2383     hideMenu.add(hideAllSelection);
2384     hideMenu.add(hideAllButSelection);
2385
2386     formatMenu.add(font);
2387     formatMenu.addSeparator();
2388     formatMenu.add(wrapMenuItem);
2389     formatMenu.add(scaleAbove);
2390     formatMenu.add(scaleLeft);
2391     formatMenu.add(scaleRight);
2392     formatMenu.add(seqLimits);
2393     formatMenu.add(idRightAlign);
2394     formatMenu.add(hiddenMarkers);
2395     formatMenu.add(viewBoxesMenuItem);
2396     formatMenu.add(viewTextMenuItem);
2397     formatMenu.add(colourTextMenuItem);
2398     formatMenu.add(renderGapsMenuItem);
2399     formatMenu.add(centreColumnLabelsMenuItem);
2400     formatMenu.add(showNonconservedMenuItem);
2401     selectMenu.add(findMenuItem);
2402     selectMenu.addSeparator();
2403     selectMenu.add(selectAllSequenceMenuItem);
2404     selectMenu.add(deselectAllSequenceMenuItem);
2405     selectMenu.add(invertSequenceMenuItem);
2406     selectMenu.add(invertColSel);
2407     selectMenu.add(createGroup);
2408     selectMenu.add(unGroup);
2409     selectMenu.add(grpsFromSelection);
2410     selectMenu.add(deleteGroups);
2411     calculateMenu.add(expandAlignment);
2412     // TODO - determine if the listenToViewSelections button is needed : see bug
2413     // JAL-574
2414     // selectMenu.addSeparator();
2415     // selectMenu.add(listenToViewSelections);
2416   }
2417
2418   /**
2419    * Action on clicking sort annotations by type.
2420    * 
2421    * @param sortOrder
2422    */
2423   protected void sortAnnotations_actionPerformed()
2424   {
2425   }
2426
2427   /**
2428    * Action on clicking Show all annotations.
2429    * 
2430    * @param forSequences
2431    *          update sequence-related annotations
2432    * @param forAlignment
2433    *          update non-sequence-related annotations
2434    */
2435   protected void showAllAnnotations_actionPerformed(boolean forSequences,
2436           boolean forAlignment)
2437   {
2438     setAnnotationsVisibility(true, forSequences, forAlignment);
2439   }
2440
2441   /**
2442    * Action on clicking Hide all annotations.
2443    * 
2444    * @param forSequences
2445    *          update sequence-related annotations
2446    * @param forAlignment
2447    *          update non-sequence-related annotations
2448    */
2449   protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2450           boolean forAlignment)
2451   {
2452     setAnnotationsVisibility(false, forSequences, forAlignment);
2453   }
2454
2455   /**
2456    * Set the visibility of annotations to true or false. Can act on
2457    * sequence-related annotations, or alignment-related, or both.
2458    * 
2459    * @param visible
2460    * @param forSequences
2461    *          update sequence-related annotations
2462    * @param forAlignment
2463    *          update non-sequence-related annotations
2464    */
2465   protected void setAnnotationsVisibility(boolean visible,
2466           boolean forSequences, boolean forAlignment)
2467   {
2468
2469   }
2470
2471   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2472   {
2473     // TODO Auto-generated method stub
2474
2475   }
2476
2477   protected void listenToViewSelections_actionPerformed(ActionEvent e)
2478   {
2479     // TODO Auto-generated method stub
2480
2481   }
2482
2483   protected void showAllhidden_actionPerformed(ActionEvent e)
2484   {
2485     // TODO Auto-generated method stub
2486
2487   }
2488
2489   protected void hideAllButSelection_actionPerformed(ActionEvent e)
2490   {
2491     // TODO Auto-generated method stub
2492
2493   }
2494
2495   protected void hideAllSelection_actionPerformed(ActionEvent e)
2496   {
2497     // TODO Auto-generated method stub
2498
2499   }
2500
2501   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2502   {
2503     // TODO Auto-generated method stub
2504
2505   }
2506
2507   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2508   {
2509     // TODO Auto-generated method stub
2510
2511   }
2512
2513   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2514   {
2515     // TODO Auto-generated method stub
2516
2517   }
2518
2519   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2520   {
2521     // TODO Auto-generated method stub
2522
2523   }
2524
2525   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2526   {
2527     // TODO Auto-generated method stub
2528
2529   }
2530
2531   protected void showGroupConservation_actionPerformed(ActionEvent e)
2532   {
2533     // TODO Auto-generated method stub
2534
2535   }
2536
2537   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2538   {
2539     // TODO Auto-generated method stub
2540
2541   }
2542
2543   protected void showSeqFeaturesHeight_actionPerformed(
2544           ActionEvent actionEvent)
2545   {
2546     // TODO Auto-generated method stub
2547
2548   }
2549
2550   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2551   {
2552     // TODO Auto-generated method stub
2553
2554   }
2555
2556   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2557   {
2558     // TODO Auto-generated method stub
2559
2560   }
2561
2562   protected void followHighlight_actionPerformed()
2563   {
2564     // TODO Auto-generated method stub
2565
2566   }
2567
2568   protected void showNpFeats_actionPerformed(ActionEvent e)
2569   {
2570     // TODO Auto-generated method stub
2571
2572   }
2573
2574   protected void showDbRefs_actionPerformed(ActionEvent e)
2575   {
2576     // TODO Auto-generated method stub
2577
2578   }
2579
2580   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2581   {
2582   }
2583
2584   protected void showProducts_actionPerformed(ActionEvent e)
2585   {
2586   }
2587
2588   protected void buildSortByAnnotationScoresMenu()
2589   {
2590   }
2591
2592   protected void extractScores_actionPerformed(ActionEvent e)
2593   {
2594   }
2595
2596   protected void outputText_actionPerformed(ActionEvent e)
2597   {
2598   }
2599
2600   public void addFromFile_actionPerformed(ActionEvent e)
2601   {
2602
2603   }
2604
2605   public void addFromText_actionPerformed(ActionEvent e)
2606   {
2607
2608   }
2609
2610   public void addFromURL_actionPerformed(ActionEvent e)
2611   {
2612
2613   }
2614
2615   public void exportFeatures_actionPerformed(ActionEvent e)
2616   {
2617
2618   }
2619
2620   public void exportAnnotations_actionPerformed(ActionEvent e)
2621   {
2622
2623   }
2624
2625   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2626   {
2627   }
2628
2629   protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2630   {
2631
2632   }
2633
2634   protected void closeMenuItem_actionPerformed(boolean b)
2635   {
2636   }
2637
2638   protected void redoMenuItem_actionPerformed(ActionEvent e)
2639   {
2640   }
2641
2642   protected void undoMenuItem_actionPerformed(ActionEvent e)
2643   {
2644   }
2645
2646   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2647   {
2648   }
2649
2650   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2651   {
2652   }
2653
2654   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2655   {
2656   }
2657
2658   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2659   {
2660   }
2661
2662   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2663   {
2664   }
2665
2666   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2667   {
2668   }
2669
2670   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2671   {
2672   }
2673
2674   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2675   {
2676   }
2677
2678   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2679   {
2680   }
2681
2682   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2683   {
2684   }
2685
2686   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2687   {
2688   }
2689
2690   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2691   {
2692   }
2693
2694   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2695   {
2696   }
2697
2698   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2699   {
2700   }
2701
2702   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2703   {
2704   }
2705
2706   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2707   {
2708   }
2709
2710   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2711   {
2712   }
2713
2714   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2715   {
2716   }
2717
2718   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2719   {
2720   }
2721
2722   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2723   {
2724   }
2725
2726   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2727   {
2728   }
2729
2730   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2731   {
2732   }
2733
2734   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2735   {
2736   }
2737
2738   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2739   {
2740   }
2741
2742   protected void clustalColour_actionPerformed(ActionEvent e)
2743   {
2744   }
2745
2746   protected void zappoColour_actionPerformed(ActionEvent e)
2747   {
2748   }
2749
2750   protected void taylorColour_actionPerformed(ActionEvent e)
2751   {
2752   }
2753
2754   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2755   {
2756   }
2757
2758   protected void helixColour_actionPerformed(ActionEvent e)
2759   {
2760   }
2761
2762   protected void strandColour_actionPerformed(ActionEvent e)
2763   {
2764   }
2765
2766   protected void turnColour_actionPerformed(ActionEvent e)
2767   {
2768   }
2769
2770   protected void buriedColour_actionPerformed(ActionEvent e)
2771   {
2772   }
2773
2774   protected void userDefinedColour_actionPerformed(ActionEvent e)
2775   {
2776   }
2777
2778   protected void PIDColour_actionPerformed(ActionEvent e)
2779   {
2780   }
2781
2782   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2783   {
2784   }
2785
2786   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2787   {
2788   }
2789
2790   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2791   {
2792   }
2793
2794   /*
2795    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2796    */
2797
2798   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2799   {
2800   }
2801
2802   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2803   {
2804   }
2805
2806   protected void printMenuItem_actionPerformed(ActionEvent e)
2807   {
2808   }
2809
2810   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2811   {
2812   }
2813
2814   protected void findMenuItem_actionPerformed(ActionEvent e)
2815   {
2816   }
2817
2818   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2819   {
2820   }
2821
2822   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2823   {
2824   }
2825
2826   protected void nucleotideColour_actionPerformed(ActionEvent e)
2827   {
2828   }
2829
2830   protected void deleteGroups_actionPerformed(ActionEvent e)
2831   {
2832   }
2833
2834   protected void createGroup_actionPerformed(ActionEvent e)
2835   {
2836   }
2837
2838   protected void unGroup_actionPerformed(ActionEvent e)
2839   {
2840   }
2841
2842   protected void copy_actionPerformed(ActionEvent e)
2843   {
2844   }
2845
2846   protected void cut_actionPerformed(ActionEvent e)
2847   {
2848   }
2849
2850   protected void delete_actionPerformed(ActionEvent e)
2851   {
2852   }
2853
2854   protected void pasteNew_actionPerformed(ActionEvent e)
2855   {
2856   }
2857
2858   protected void pasteThis_actionPerformed(ActionEvent e)
2859   {
2860   }
2861
2862   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2863   {
2864   }
2865
2866   public void createPNG(java.io.File f)
2867   {
2868   }
2869
2870   protected void font_actionPerformed(ActionEvent e)
2871   {
2872   }
2873
2874   protected void seqLimit_actionPerformed(ActionEvent e)
2875   {
2876   }
2877
2878   public void seqDBRef_actionPerformed(ActionEvent e)
2879   {
2880
2881   }
2882
2883   public void createEPS(java.io.File f)
2884   {
2885   }
2886
2887   public void createSVG(java.io.File f)
2888   {
2889
2890   }
2891   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2892   {
2893
2894   }
2895
2896   /**
2897    * Template method to handle the 'load T-Coffee scores' menu event.
2898    * <p>
2899    * Subclasses override this method to provide a custom action.
2900    * 
2901    * @param event
2902    *          The raised event
2903    */
2904   protected void loadScores_actionPerformed(ActionEvent event)
2905   {
2906
2907   }
2908
2909   /**
2910    * Template method to handle the 'Color T-Coffee scores' menu event.
2911    * <p>
2912    * Subclasses override this method to provide a custom action.
2913    * 
2914    * @param event
2915    *          The raised event
2916    */
2917   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2918   {
2919
2920   }
2921
2922   protected void jpred_actionPerformed(ActionEvent e)
2923   {
2924   }
2925
2926   protected void scaleAbove_actionPerformed(ActionEvent e)
2927   {
2928   }
2929
2930   protected void scaleLeft_actionPerformed(ActionEvent e)
2931   {
2932   }
2933
2934   protected void scaleRight_actionPerformed(ActionEvent e)
2935   {
2936   }
2937
2938   protected void modifyPID_actionPerformed(ActionEvent e)
2939   {
2940   }
2941
2942   protected void modifyConservation_actionPerformed(ActionEvent e)
2943   {
2944   }
2945
2946   protected void saveAs_actionPerformed(ActionEvent e)
2947   {
2948   }
2949
2950   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2951   {
2952   }
2953
2954   public void vamsasStore_actionPerformed(ActionEvent e)
2955   {
2956
2957   }
2958
2959   public void vamsasLoad_actionPerformed(ActionEvent e)
2960   {
2961
2962   }
2963
2964   public void showTranslation_actionPerformed(ActionEvent e)
2965   {
2966
2967   }
2968
2969   public void featureSettings_actionPerformed(ActionEvent e)
2970   {
2971
2972   }
2973
2974   public void fetchSequence_actionPerformed(ActionEvent e)
2975   {
2976
2977   }
2978
2979   public void smoothFont_actionPerformed(ActionEvent e)
2980   {
2981
2982   }
2983
2984   public void annotationColour_actionPerformed(ActionEvent e)
2985   {
2986
2987   }
2988
2989   public void rnahelicesColour_actionPerformed(ActionEvent e)
2990   {
2991
2992   }
2993
2994   public void associatedData_actionPerformed(ActionEvent e)
2995   {
2996
2997   }
2998
2999   public void autoCalculate_actionPerformed(ActionEvent e)
3000   {
3001
3002   }
3003
3004   public void sortByTreeOption_actionPerformed(ActionEvent e)
3005   {
3006
3007   }
3008
3009   public void showAllSeqs_actionPerformed(ActionEvent e)
3010   {
3011
3012   }
3013
3014   public void showAllColumns_actionPerformed(ActionEvent e)
3015   {
3016
3017   }
3018
3019   public void hideSelSequences_actionPerformed(ActionEvent e)
3020   {
3021
3022   }
3023
3024   public void hideSelColumns_actionPerformed(ActionEvent e)
3025   {
3026
3027   }
3028
3029   public void hiddenMarkers_actionPerformed(ActionEvent e)
3030   {
3031
3032   }
3033
3034   public void findPdbId_actionPerformed(ActionEvent e)
3035   {
3036
3037   }
3038
3039   public void enterPdbId_actionPerformed(ActionEvent e)
3040   {
3041
3042   }
3043
3044   public void pdbFile_actionPerformed(ActionEvent e)
3045   {
3046
3047   }
3048
3049   public void invertColSel_actionPerformed(ActionEvent e)
3050   {
3051
3052   }
3053
3054   public void tabSelectionChanged(int sel)
3055   {
3056
3057   }
3058
3059   public void tabbedPane_mousePressed(MouseEvent e)
3060   {
3061
3062   }
3063
3064   public void tabbedPane_focusGained(FocusEvent e)
3065   {
3066     requestFocus();
3067   }
3068
3069   public void save_actionPerformed(ActionEvent e)
3070   {
3071
3072   }
3073
3074   public void reload_actionPerformed(ActionEvent e)
3075   {
3076
3077   }
3078
3079   public void newView_actionPerformed(ActionEvent e)
3080   {
3081
3082   }
3083
3084   public void textColour_actionPerformed(ActionEvent e)
3085   {
3086
3087   }
3088
3089   public void idRightAlign_actionPerformed(ActionEvent e)
3090   {
3091
3092   }
3093
3094   public void expandViews_actionPerformed(ActionEvent e)
3095   {
3096
3097   }
3098
3099   public void gatherViews_actionPerformed(ActionEvent e)
3100   {
3101
3102   }
3103
3104   public void buildTreeMenu()
3105   {
3106
3107   }
3108
3109   public void pageSetup_actionPerformed(ActionEvent e)
3110   {
3111
3112   }
3113
3114   public void alignmentProperties()
3115   {
3116
3117   }
3118
3119   protected void expand_newalign(ActionEvent e)
3120   {
3121     // TODO Auto-generated method stub
3122
3123   }
3124
3125   protected boolean isShowAutoCalculatedAbove()
3126   {
3127     return showAutoCalculatedAbove;
3128   }
3129
3130   protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3131   {
3132     this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3133   }
3134
3135   protected SequenceAnnotationOrder getAnnotationSortOrder()
3136   {
3137     return annotationSortOrder;
3138   }
3139
3140   protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3141   {
3142     this.annotationSortOrder = annotationSortOrder;
3143   }
3144 }