Remove edit menu if no group defined
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
1 /*\r
2  * Jalview - A Sequence Alignment Editor and Viewer\r
3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
4  *\r
5  * This program is free software; you can redistribute it and/or\r
6  * modify it under the terms of the GNU General Public License\r
7  * as published by the Free Software Foundation; either version 2\r
8  * of the License, or (at your option) any later version.\r
9  *\r
10  * This program is distributed in the hope that it will be useful,\r
11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
13  * GNU General Public License for more details.\r
14  *\r
15  * You should have received a copy of the GNU General Public License\r
16  * along with this program; if not, write to the Free Software\r
17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
18  */\r
19 package jalview.jbgui;\r
20 \r
21 import java.awt.*;\r
22 import java.awt.event.*;\r
23 import javax.swing.*;\r
24 \r
25 import jalview.schemes.*;\r
26 \r
27 public class GAlignFrame\r
28     extends JInternalFrame\r
29 {\r
30   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
31   protected JMenu fileMenu = new JMenu();\r
32   protected JMenuItem closeMenuItem = new JMenuItem();\r
33   protected JMenu editMenu = new JMenu();\r
34   protected JMenu viewMenu = new JMenu();\r
35   protected JMenu colourMenu = new JMenu();\r
36   protected JMenu calculateMenu = new JMenu();\r
37   protected JMenu webService = new JMenu();\r
38   protected JMenuItem webServiceNoServices;\r
39   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
40   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
41   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
42   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
43   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
44   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
45   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
46   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
47   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
48   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
49   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
50   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
51   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
52   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
53   protected JMenuItem PCAMenuItem = new JMenuItem();\r
54   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
55   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
56   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
57   BorderLayout borderLayout1 = new BorderLayout();\r
58   public JLabel statusBar = new JLabel();\r
59   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
60   protected JMenu outputTextboxMenu = new JMenu();\r
61   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
62   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
63   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
64   protected JRadioButtonMenuItem hydrophobicityColour = new\r
65       JRadioButtonMenuItem();\r
66   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
67   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
68   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
69   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
70   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
71   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
72   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
73   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
74   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
75   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
76   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
77   JMenuItem htmlMenuItem = new JMenuItem();\r
78   JMenuItem overviewMenuItem = new JMenuItem();\r
79   protected JMenuItem undoMenuItem = new JMenuItem();\r
80   protected JMenuItem redoMenuItem = new JMenuItem();\r
81   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
82   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
83   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
84   JMenuItem printMenuItem = new JMenuItem();\r
85   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
86   JMenuItem findMenuItem = new JMenuItem();\r
87   JMenu searchMenu = new JMenu();\r
88   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
89   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
90   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
91   JMenuItem deleteGroups = new JMenuItem();\r
92   JMenuItem delete = new JMenuItem();\r
93   JMenuItem copy = new JMenuItem();\r
94   JMenuItem cut = new JMenuItem();\r
95   JMenu jMenu1 = new JMenu();\r
96   JMenuItem pasteNew = new JMenuItem();\r
97   JMenuItem pasteThis = new JMenuItem();\r
98   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
99   JMenuItem createPNG = new JMenuItem();\r
100   protected JMenuItem font = new JMenuItem();\r
101   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
102   JMenuItem epsFile = new JMenuItem();\r
103   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
104   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
105   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
106   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
107   protected JMenuItem modifyPID = new JMenuItem();\r
108   protected JMenuItem modifyConservation = new JMenuItem();\r
109   protected JMenu sortByTreeMenu = new JMenu();\r
110   protected JMenu sort = new JMenu();\r
111   JMenu calculate = new JMenu();\r
112   JMenu jMenu2 = new JMenu();\r
113   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
114   protected ButtonGroup colours = new ButtonGroup();\r
115   JMenuItem vamsasStore = new JMenuItem();\r
116   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
117   //protected JTabbedPane tabbedPane = new JTabbedPane();\r
118   public JMenuItem featureSettings = new JMenuItem();\r
119   JMenuItem fetchSequence = new JMenuItem();\r
120   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
121   JMenuItem annotationColour = new JMenuItem();\r
122   JMenuItem fetchSeqFeatures = new JMenuItem();\r
123 \r
124 \r
125 \r
126   JMenuItem associatedData = new JMenuItem();\r
127   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
128   public GAlignFrame()\r
129   {\r
130 \r
131 \r
132     try\r
133     {\r
134       jbInit();\r
135       setJMenuBar(alignFrameMenuBar);\r
136 \r
137       // dynamically fill save as menu with available formats\r
138       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
139       {\r
140         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
141                              elementAt(\r
142                                  i));\r
143         item.addActionListener(new java.awt.event.ActionListener()\r
144         {\r
145           public void actionPerformed(ActionEvent e)\r
146           {\r
147             outputText_actionPerformed(e);\r
148           }\r
149         });\r
150 \r
151         outputTextboxMenu.add(item);\r
152       }\r
153     }\r
154     catch (Exception e)\r
155     {\r
156     }\r
157 \r
158 \r
159     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
160     {\r
161       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
162           getUserColourSchemes().keys();\r
163 \r
164       while (userColours.hasMoreElements())\r
165       {\r
166         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
167             nextElement().toString());\r
168         radioItem.setName("USER_DEFINED");\r
169         radioItem.addMouseListener(new MouseAdapter()\r
170             {\r
171               public void mousePressed(MouseEvent evt)\r
172               {\r
173                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
174                 {\r
175                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
176 \r
177                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
178                       "Remove from default list?",\r
179                       "Remove user defined colour",\r
180                       JOptionPane.YES_NO_OPTION);\r
181                   if(option == JOptionPane.YES_OPTION)\r
182                   {\r
183                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
184                     colourMenu.remove(radioItem);\r
185                   }\r
186                   else\r
187                     radioItem.addActionListener(new ActionListener()\r
188                     {\r
189                       public void actionPerformed(ActionEvent evt)\r
190                       {\r
191                         userDefinedColour_actionPerformed(evt);\r
192                       }\r
193                     });\r
194                 }\r
195               }\r
196             });\r
197         radioItem.addActionListener(new ActionListener()\r
198         {\r
199           public void actionPerformed(ActionEvent evt)\r
200           {\r
201             userDefinedColour_actionPerformed(evt);\r
202           }\r
203         });\r
204         colourMenu.insert(radioItem, 15);\r
205         colours.add(radioItem);\r
206       }\r
207     }\r
208     colours.add(noColourmenuItem);\r
209     colours.add(clustalColour);\r
210     colours.add(zappoColour);\r
211     colours.add(taylorColour);\r
212     colours.add(hydrophobicityColour);\r
213     colours.add(helixColour);\r
214     colours.add(strandColour);\r
215     colours.add(turnColour);\r
216     colours.add(buriedColour);\r
217     colours.add(userDefinedColour);\r
218     colours.add(PIDColour);\r
219     colours.add(BLOSUM62Colour);\r
220     colours.add(nucleotideColour);\r
221 \r
222     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
223 \r
224 \r
225   }\r
226 \r
227   public void setColourSelected(String defaultColour)\r
228   {\r
229 \r
230     if (defaultColour != null)\r
231     {\r
232       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
233 \r
234       switch (index)\r
235       {\r
236         case ColourSchemeProperty.NONE:\r
237               noColourmenuItem.setSelected(true);\r
238               break;\r
239         case ColourSchemeProperty.CLUSTAL:\r
240           clustalColour.setSelected(true);\r
241 \r
242           break;\r
243 \r
244         case ColourSchemeProperty.BLOSUM:\r
245           BLOSUM62Colour.setSelected(true);\r
246 \r
247           break;\r
248 \r
249         case ColourSchemeProperty.PID:\r
250           PIDColour.setSelected(true);\r
251 \r
252           break;\r
253 \r
254         case ColourSchemeProperty.ZAPPO:\r
255           zappoColour.setSelected(true);\r
256 \r
257           break;\r
258 \r
259         case ColourSchemeProperty.TAYLOR:\r
260           taylorColour.setSelected(true);\r
261           break;\r
262 \r
263         case ColourSchemeProperty.HYDROPHOBIC:\r
264           hydrophobicityColour.setSelected(true);\r
265 \r
266           break;\r
267 \r
268         case ColourSchemeProperty.HELIX:\r
269           helixColour.setSelected(true);\r
270 \r
271           break;\r
272 \r
273         case ColourSchemeProperty.STRAND:\r
274           strandColour.setSelected(true);\r
275 \r
276           break;\r
277 \r
278         case ColourSchemeProperty.TURN:\r
279           turnColour.setSelected(true);\r
280 \r
281           break;\r
282 \r
283         case ColourSchemeProperty.BURIED:\r
284           buriedColour.setSelected(true);\r
285 \r
286           break;\r
287 \r
288         case ColourSchemeProperty.NUCLEOTIDE:\r
289           nucleotideColour.setSelected(true);\r
290 \r
291           break;\r
292 \r
293         case ColourSchemeProperty.USER_DEFINED:\r
294           userDefinedColour.setSelected(true);\r
295 \r
296           break;\r
297       }\r
298     }\r
299 \r
300   }\r
301 \r
302   private void jbInit()\r
303       throws Exception\r
304   {\r
305     fileMenu.setMnemonic('F');\r
306     fileMenu.setText("File");\r
307     saveAlignmentMenu.setMnemonic('L');\r
308     saveAlignmentMenu.setText("Save As");\r
309     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
310         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
311     saveAlignmentMenu.addActionListener(new ActionListener()\r
312     {\r
313       public void actionPerformed(ActionEvent e)\r
314       {\r
315         saveAlignmentMenu_actionPerformed(e);\r
316       }\r
317     });\r
318     closeMenuItem.setMnemonic('C');\r
319     closeMenuItem.setText("Close");\r
320     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
321     {\r
322       public void actionPerformed(ActionEvent e)\r
323       {\r
324         closeMenuItem_actionPerformed(e);\r
325       }\r
326     });\r
327     editMenu.setText("Edit");\r
328     viewMenu.setText("View");\r
329     colourMenu.setText("Colour");\r
330     calculateMenu.setText("Calculate");\r
331     webService.setText("Web Service");\r
332     selectAllSequenceMenuItem.setText("Select all");\r
333     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
334         java.awt.event.KeyEvent.VK_A,\r
335         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
336     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
337                                                 ActionListener()\r
338     {\r
339       public void actionPerformed(ActionEvent e)\r
340       {\r
341         selectAllSequenceMenuItem_actionPerformed(e);\r
342       }\r
343     });\r
344     deselectAllSequenceMenuItem.setText("Deselect All");\r
345     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
346                                                getKeyStroke(\r
347         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
348     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
349                                                   ActionListener()\r
350     {\r
351       public void actionPerformed(ActionEvent e)\r
352       {\r
353         deselectAllSequenceMenuItem_actionPerformed(e);\r
354       }\r
355     });\r
356     invertSequenceMenuItem.setText("Invert Selection");\r
357     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
358     {\r
359       public void actionPerformed(ActionEvent e)\r
360       {\r
361         invertSequenceMenuItem_actionPerformed(e);\r
362       }\r
363     });\r
364     remove2LeftMenuItem.setText("Remove Left");\r
365     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
366     {\r
367       public void actionPerformed(ActionEvent e)\r
368       {\r
369         remove2LeftMenuItem_actionPerformed(e);\r
370       }\r
371     });\r
372     remove2RightMenuItem.setText("Remove Right");\r
373     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
374     {\r
375       public void actionPerformed(ActionEvent e)\r
376       {\r
377         remove2RightMenuItem_actionPerformed(e);\r
378       }\r
379     });\r
380     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
381     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
382                                                  ActionListener()\r
383     {\r
384       public void actionPerformed(ActionEvent e)\r
385       {\r
386         removeGappedColumnMenuItem_actionPerformed(e);\r
387       }\r
388     });\r
389     removeAllGapsMenuItem.setText("Remove All Gaps");\r
390     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
391     {\r
392       public void actionPerformed(ActionEvent e)\r
393       {\r
394         removeAllGapsMenuItem_actionPerformed(e);\r
395       }\r
396     });\r
397     viewBoxesMenuItem.setText("Boxes");\r
398     viewBoxesMenuItem.setState(true);\r
399     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
400     {\r
401       public void actionPerformed(ActionEvent e)\r
402       {\r
403         viewBoxesMenuItem_actionPerformed(e);\r
404       }\r
405     });\r
406     viewTextMenuItem.setText("Text");\r
407     viewTextMenuItem.setState(true);\r
408     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
409     {\r
410       public void actionPerformed(ActionEvent e)\r
411       {\r
412         viewTextMenuItem_actionPerformed(e);\r
413       }\r
414     });\r
415     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
416     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
417     {\r
418       public void actionPerformed(ActionEvent e)\r
419       {\r
420         sortPairwiseMenuItem_actionPerformed(e);\r
421       }\r
422     });\r
423     sortIDMenuItem.setText("by ID");\r
424     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
425     {\r
426       public void actionPerformed(ActionEvent e)\r
427       {\r
428         sortIDMenuItem_actionPerformed(e);\r
429       }\r
430     });\r
431     sortGroupMenuItem.setText("by Group");\r
432     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
433     {\r
434       public void actionPerformed(ActionEvent e)\r
435       {\r
436         sortGroupMenuItem_actionPerformed(e);\r
437       }\r
438     });\r
439     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
440     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
441                                                ActionListener()\r
442     {\r
443       public void actionPerformed(ActionEvent e)\r
444       {\r
445         removeRedundancyMenuItem_actionPerformed(e);\r
446       }\r
447     });\r
448     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
449     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
450                                                 ActionListener()\r
451     {\r
452       public void actionPerformed(ActionEvent e)\r
453       {\r
454         pairwiseAlignmentMenuItem_actionPerformed(e);\r
455       }\r
456     });\r
457     PCAMenuItem.setText("Principal Component Analysis");\r
458     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
459     {\r
460       public void actionPerformed(ActionEvent e)\r
461       {\r
462         PCAMenuItem_actionPerformed(e);\r
463       }\r
464     });\r
465     averageDistanceTreeMenuItem.setText(\r
466         "Average Distance Using % Identity");\r
467     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
468                                                   ActionListener()\r
469     {\r
470       public void actionPerformed(ActionEvent e)\r
471       {\r
472         averageDistanceTreeMenuItem_actionPerformed(e);\r
473       }\r
474     });\r
475     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
476     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
477     {\r
478       public void actionPerformed(ActionEvent e)\r
479       {\r
480         neighbourTreeMenuItem_actionPerformed(e);\r
481       }\r
482     });\r
483     this.getContentPane().setLayout(borderLayout1);\r
484     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
485     statusBar.setBackground(Color.white);\r
486     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
487     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
488     statusBar.setText("Status bar");\r
489     outputTextboxMenu.setMnemonic('T');\r
490     outputTextboxMenu.setText("Output to Textbox");\r
491     clustalColour.setText("Clustalx");\r
492 \r
493     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
494     {\r
495       public void actionPerformed(ActionEvent e)\r
496       {\r
497         clustalColour_actionPerformed(e);\r
498       }\r
499     });\r
500     zappoColour.setText("Zappo");\r
501     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
502     {\r
503       public void actionPerformed(ActionEvent e)\r
504       {\r
505         zappoColour_actionPerformed(e);\r
506       }\r
507     });\r
508     taylorColour.setText("Taylor");\r
509     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
510     {\r
511       public void actionPerformed(ActionEvent e)\r
512       {\r
513         taylorColour_actionPerformed(e);\r
514       }\r
515     });\r
516     hydrophobicityColour.setText("Hydrophobicity");\r
517     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
518     {\r
519       public void actionPerformed(ActionEvent e)\r
520       {\r
521         hydrophobicityColour_actionPerformed(e);\r
522       }\r
523     });\r
524     helixColour.setText("Helix Propensity");\r
525     helixColour.addActionListener(new java.awt.event.ActionListener()\r
526     {\r
527       public void actionPerformed(ActionEvent e)\r
528       {\r
529         helixColour_actionPerformed(e);\r
530       }\r
531     });\r
532     strandColour.setText("Strand Propensity");\r
533     strandColour.addActionListener(new java.awt.event.ActionListener()\r
534     {\r
535       public void actionPerformed(ActionEvent e)\r
536       {\r
537         strandColour_actionPerformed(e);\r
538       }\r
539     });\r
540     turnColour.setText("Turn Propensity");\r
541     turnColour.addActionListener(new java.awt.event.ActionListener()\r
542     {\r
543       public void actionPerformed(ActionEvent e)\r
544       {\r
545         turnColour_actionPerformed(e);\r
546       }\r
547     });\r
548     buriedColour.setText("Buried Index");\r
549     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
550     {\r
551       public void actionPerformed(ActionEvent e)\r
552       {\r
553         buriedColour_actionPerformed(e);\r
554       }\r
555     });\r
556     userDefinedColour.setText("User Defined...");\r
557     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
558     {\r
559       public void actionPerformed(ActionEvent e)\r
560       {\r
561         userDefinedColour_actionPerformed(e);\r
562       }\r
563     });\r
564     PIDColour.setText("Percentage Identity");\r
565     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
566     {\r
567       public void actionPerformed(ActionEvent e)\r
568       {\r
569         PIDColour_actionPerformed(e);\r
570       }\r
571     });\r
572     BLOSUM62Colour.setText("BLOSUM62 Score");\r
573     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
574     {\r
575       public void actionPerformed(ActionEvent e)\r
576       {\r
577         BLOSUM62Colour_actionPerformed(e);\r
578       }\r
579     });\r
580     avDistanceTreeBlosumMenuItem.setText(\r
581         "Average Distance Using BLOSUM62");\r
582     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
583         ActionListener()\r
584     {\r
585       public void actionPerformed(ActionEvent e)\r
586       {\r
587         avTreeBlosumMenuItem_actionPerformed(e);\r
588       }\r
589     });\r
590     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
591     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
592     {\r
593       public void actionPerformed(ActionEvent e)\r
594       {\r
595         njTreeBlosumMenuItem_actionPerformed(e);\r
596       }\r
597     });\r
598     annotationPanelMenuItem.setActionCommand("");\r
599     annotationPanelMenuItem.setText("Show Annotations");\r
600     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
601     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
602     {\r
603       public void actionPerformed(ActionEvent e)\r
604       {\r
605         annotationPanelMenuItem_actionPerformed(e);\r
606       }\r
607     });\r
608     colourTextMenuItem.setText("Colour Text");\r
609     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
610     {\r
611       public void actionPerformed(ActionEvent e)\r
612       {\r
613         colourTextMenuItem_actionPerformed(e);\r
614       }\r
615     });\r
616     htmlMenuItem.setText("HTML");\r
617     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
618     {\r
619       public void actionPerformed(ActionEvent e)\r
620       {\r
621         htmlMenuItem_actionPerformed(e);\r
622       }\r
623     });\r
624     overviewMenuItem.setText("Overview Window");\r
625     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
626     {\r
627       public void actionPerformed(ActionEvent e)\r
628       {\r
629         overviewMenuItem_actionPerformed(e);\r
630       }\r
631     });\r
632     undoMenuItem.setEnabled(false);\r
633     undoMenuItem.setMnemonic('Z');\r
634     undoMenuItem.setText("Undo");\r
635     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
636         java.awt.event.KeyEvent.VK_Z,\r
637         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
638     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
639     {\r
640       public void actionPerformed(ActionEvent e)\r
641       {\r
642         undoMenuItem_actionPerformed(e);\r
643       }\r
644     });\r
645     redoMenuItem.setEnabled(false);\r
646     redoMenuItem.setMnemonic('0');\r
647     redoMenuItem.setText("Redo");\r
648     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
649     {\r
650       public void actionPerformed(ActionEvent e)\r
651       {\r
652         redoMenuItem_actionPerformed(e);\r
653       }\r
654     });\r
655     conservationMenuItem.setText("By Conservation");\r
656     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
657     {\r
658       public void actionPerformed(ActionEvent e)\r
659       {\r
660         conservationMenuItem_actionPerformed(e);\r
661       }\r
662     });\r
663     noColourmenuItem.setText("None");\r
664     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
665     {\r
666       public void actionPerformed(ActionEvent e)\r
667       {\r
668         noColourmenuItem_actionPerformed(e);\r
669       }\r
670     });\r
671     wrapMenuItem.setText("Wrap");\r
672     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
673     {\r
674       public void actionPerformed(ActionEvent e)\r
675       {\r
676         wrapMenuItem_actionPerformed(e);\r
677       }\r
678     });\r
679     printMenuItem.setText("Print");\r
680     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
681     {\r
682       public void actionPerformed(ActionEvent e)\r
683       {\r
684         printMenuItem_actionPerformed(e);\r
685       }\r
686     });\r
687     renderGapsMenuItem.setText("Show Gaps");\r
688     renderGapsMenuItem.setState(true);\r
689     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
690     {\r
691       public void actionPerformed(ActionEvent e)\r
692       {\r
693         renderGapsMenuItem_actionPerformed(e);\r
694       }\r
695     });\r
696     findMenuItem.setText("Find...");\r
697     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
698         java.awt.event.KeyEvent.VK_F,\r
699         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
700     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
701     {\r
702       public void actionPerformed(ActionEvent e)\r
703       {\r
704         findMenuItem_actionPerformed(e);\r
705       }\r
706     });\r
707     searchMenu.setText("Search");\r
708 \r
709     abovePIDThreshold.setText("Above Identity Threshold");\r
710     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
711     {\r
712       public void actionPerformed(ActionEvent e)\r
713       {\r
714         abovePIDThreshold_actionPerformed(e);\r
715       }\r
716     });\r
717     showSeqFeatures.setText("Show Sequence Features");\r
718     showSeqFeatures.addActionListener(new ActionListener()\r
719     {\r
720       public void actionPerformed(ActionEvent actionEvent)\r
721       {\r
722         showSeqFeatures_actionPerformed(actionEvent);\r
723       }\r
724     });\r
725     nucleotideColour.setText("Nucleotide");\r
726     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
727     {\r
728       public void actionPerformed(ActionEvent e)\r
729       {\r
730         nucleotideColour_actionPerformed(e);\r
731       }\r
732     });\r
733     deleteGroups.setText("Undefine groups");\r
734     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
735     {\r
736       public void actionPerformed(ActionEvent e)\r
737       {\r
738         deleteGroups_actionPerformed(e);\r
739       }\r
740     });\r
741     copy.setText("Copy");\r
742     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
743         java.awt.event.KeyEvent.VK_C,\r
744         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
745     copy.setMnemonic(KeyEvent.VK_C);\r
746 \r
747     copy.addActionListener(new java.awt.event.ActionListener()\r
748     {\r
749       public void actionPerformed(ActionEvent e)\r
750       {\r
751         copy_actionPerformed(e);\r
752       }\r
753     });\r
754     cut.setText("Cut");\r
755     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
756         java.awt.event.KeyEvent.VK_X,\r
757         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
758     cut.setMnemonic(KeyEvent.VK_X);\r
759     cut.addActionListener(new java.awt.event.ActionListener()\r
760     {\r
761       public void actionPerformed(ActionEvent e)\r
762       {\r
763         cut_actionPerformed(e);\r
764       }\r
765     });\r
766     delete.setText("Delete");\r
767     delete.addActionListener(new java.awt.event.ActionListener()\r
768     {\r
769       public void actionPerformed(ActionEvent e)\r
770       {\r
771         delete_actionPerformed(e);\r
772       }\r
773     });\r
774     jMenu1.setMnemonic('V');\r
775     jMenu1.setText("Paste");\r
776     pasteNew.setText("To New Alignment");\r
777     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
778         java.awt.event.KeyEvent.VK_V,\r
779         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
780     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
781     {\r
782       public void actionPerformed(ActionEvent e)\r
783       {\r
784         pasteNew_actionPerformed(e);\r
785       }\r
786     });\r
787     pasteThis.setText("Add To This Alignment");\r
788     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
789     {\r
790       public void actionPerformed(ActionEvent e)\r
791       {\r
792         pasteThis_actionPerformed(e);\r
793       }\r
794     });\r
795     applyToAllGroups.setText("Apply Colour To All Groups");\r
796     applyToAllGroups.setState(true);\r
797     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
798     {\r
799       public void actionPerformed(ActionEvent e)\r
800       {\r
801         applyToAllGroups_actionPerformed(e);\r
802       }\r
803     });\r
804     createPNG.addActionListener(new java.awt.event.ActionListener()\r
805     {\r
806       public void actionPerformed(ActionEvent e)\r
807       {\r
808         createPNG(null);\r
809       }\r
810     });\r
811     createPNG.setActionCommand("Save As PNG Image");\r
812     createPNG.setText("PNG");\r
813     font.setText("Font...");\r
814     font.addActionListener(new java.awt.event.ActionListener()\r
815     {\r
816       public void actionPerformed(ActionEvent e)\r
817       {\r
818         font_actionPerformed(e);\r
819       }\r
820     });\r
821 \r
822     seqLimits.setText("Show Sequence Limits");\r
823     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
824     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
825     {\r
826       public void actionPerformed(ActionEvent e)\r
827       {\r
828         seqLimit_actionPerformed(e);\r
829       }\r
830     });\r
831     epsFile.setText("EPS");\r
832     epsFile.addActionListener(new java.awt.event.ActionListener()\r
833     {\r
834       public void actionPerformed(ActionEvent e)\r
835       {\r
836         createEPS(null);\r
837       }\r
838     });\r
839     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
840     LoadtreeMenuItem.setText("Load Associated Tree");\r
841     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
842     {\r
843       public void actionPerformed(ActionEvent e)\r
844       {\r
845         LoadtreeMenuItem_actionPerformed(e);\r
846       }\r
847     });\r
848     scaleAbove.setVisible(false);\r
849     scaleAbove.setText("Scale Above");\r
850     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
851     {\r
852       public void actionPerformed(ActionEvent e)\r
853       {\r
854         scaleAbove_actionPerformed(e);\r
855       }\r
856     });\r
857     scaleLeft.setVisible(false);\r
858     scaleLeft.setSelected(true);\r
859     scaleLeft.setText("Scale Left");\r
860     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
861     {\r
862       public void actionPerformed(ActionEvent e)\r
863       {\r
864         scaleLeft_actionPerformed(e);\r
865       }\r
866     });\r
867     scaleRight.setVisible(false);\r
868     scaleRight.setSelected(true);\r
869     scaleRight.setText("Scale Right");\r
870     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
871     {\r
872       public void actionPerformed(ActionEvent e)\r
873       {\r
874         scaleRight_actionPerformed(e);\r
875       }\r
876     });\r
877     modifyPID.setText("Modify Identity Threshold...");\r
878     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
879     {\r
880       public void actionPerformed(ActionEvent e)\r
881       {\r
882         modifyPID_actionPerformed(e);\r
883       }\r
884     });\r
885     modifyConservation.setText("Modify Conservation Threshold...");\r
886     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
887     {\r
888       public void actionPerformed(ActionEvent e)\r
889       {\r
890         modifyConservation_actionPerformed(e);\r
891       }\r
892     });\r
893     sortByTreeMenu.setText("By Tree Order");\r
894     sort.setText("Sort");\r
895     calculate.setText("Calculate Tree");\r
896 \r
897     jMenu2.setText("Export");\r
898     padGapsMenuitem.setText("Pad Gaps");\r
899     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
900     padGapsMenuitem.addActionListener(new ActionListener()\r
901     {\r
902       public void actionPerformed(ActionEvent e)\r
903       {\r
904         padGapsMenuitem_actionPerformed(e);\r
905       }\r
906     });\r
907     vamsasStore.setVisible(false);\r
908     vamsasStore.setText("VAMSAS store");\r
909     vamsasStore.addActionListener(new ActionListener()\r
910     {\r
911       public void actionPerformed(ActionEvent e)\r
912       {\r
913         vamsasStore_actionPerformed(e);\r
914       }\r
915     });\r
916     showTranslation.setText("Translate cDNA");\r
917     showTranslation.addActionListener(new ActionListener()\r
918     {\r
919       public void actionPerformed(ActionEvent e)\r
920       {\r
921         showTranslation_actionPerformed(e);\r
922       }\r
923     });\r
924 \r
925    /* tabbedPane.addChangeListener(new ChangeListener()\r
926         {\r
927           public void stateChanged(ChangeEvent ece)\r
928           {\r
929 \r
930             tabSelected();\r
931           }\r
932         });*/\r
933     featureSettings.setText("Feature Settings...");\r
934     featureSettings.addActionListener(new ActionListener()\r
935     {\r
936       public void actionPerformed(ActionEvent e)\r
937       {\r
938         featureSettings_actionPerformed(e);\r
939       }\r
940     });\r
941     fetchSequence.setText("Fetch Sequence(s)...");\r
942     fetchSequence.addActionListener(new ActionListener()\r
943     {\r
944       public void actionPerformed(ActionEvent e)\r
945       {\r
946         fetchSequence_actionPerformed(e);\r
947       }\r
948     });\r
949     smoothFont.setText("Smooth Fonts");\r
950     smoothFont.addActionListener(new ActionListener()\r
951     {\r
952       public void actionPerformed(ActionEvent e)\r
953       {\r
954         smoothFont_actionPerformed(e);\r
955       }\r
956     });\r
957     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
958     annotationColour.setText("By Annotation...");\r
959     annotationColour.addActionListener(new ActionListener()\r
960     {\r
961       public void actionPerformed(ActionEvent e)\r
962       {\r
963         annotationColour_actionPerformed(e);\r
964       }\r
965     });\r
966     fetchSeqFeatures.setText("Fetch Sequence Features");\r
967     fetchSeqFeatures.addActionListener(new ActionListener()\r
968     {\r
969       public void actionPerformed(ActionEvent e)\r
970       {\r
971         fetchSeqFeatures_actionPerformed(e);\r
972       }\r
973     });\r
974     associatedData.setText("Load Features / Annotations");\r
975     associatedData.addActionListener(new ActionListener()\r
976     {\r
977       public void actionPerformed(ActionEvent e)\r
978       {\r
979         associatedData_actionPerformed(e);\r
980       }\r
981     });\r
982     autoCalculate.setText("Autocalculate Consensus");\r
983     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
984     autoCalculate.addActionListener(new ActionListener()\r
985     {\r
986       public void actionPerformed(ActionEvent e)\r
987       {\r
988         autoCalculate_actionPerformed(e);\r
989       }\r
990     });\r
991     alignFrameMenuBar.add(fileMenu);\r
992     alignFrameMenuBar.add(editMenu);\r
993     alignFrameMenuBar.add(searchMenu);\r
994     alignFrameMenuBar.add(viewMenu);\r
995     alignFrameMenuBar.add(colourMenu);\r
996     alignFrameMenuBar.add(calculateMenu);\r
997     alignFrameMenuBar.add(webService);\r
998     fileMenu.add(fetchSequence);\r
999     fileMenu.addSeparator();\r
1000     fileMenu.add(vamsasStore);\r
1001     fileMenu.add(saveAlignmentMenu);\r
1002     fileMenu.add(jMenu2);\r
1003     fileMenu.add(outputTextboxMenu);\r
1004     fileMenu.add(printMenuItem);\r
1005     fileMenu.addSeparator();\r
1006     fileMenu.add(LoadtreeMenuItem);\r
1007     fileMenu.add(associatedData);\r
1008     fileMenu.addSeparator();\r
1009     fileMenu.add(closeMenuItem);\r
1010     editMenu.add(undoMenuItem);\r
1011     editMenu.add(redoMenuItem);\r
1012     editMenu.add(cut);\r
1013     editMenu.add(copy);\r
1014     editMenu.add(jMenu1);\r
1015     editMenu.add(delete);\r
1016     editMenu.addSeparator();\r
1017     editMenu.add(selectAllSequenceMenuItem);\r
1018     editMenu.add(deselectAllSequenceMenuItem);\r
1019     editMenu.add(invertSequenceMenuItem);\r
1020     editMenu.add(deleteGroups);\r
1021     editMenu.addSeparator();\r
1022     editMenu.add(remove2LeftMenuItem);\r
1023     editMenu.add(remove2RightMenuItem);\r
1024     editMenu.add(removeGappedColumnMenuItem);\r
1025     editMenu.add(removeAllGapsMenuItem);\r
1026     editMenu.add(removeRedundancyMenuItem);\r
1027     editMenu.addSeparator();\r
1028     editMenu.add(padGapsMenuitem);\r
1029     searchMenu.add(findMenuItem);\r
1030     viewMenu.add(font);\r
1031     viewMenu.add(smoothFont);\r
1032     viewMenu.addSeparator();\r
1033     viewMenu.add(wrapMenuItem);\r
1034     viewMenu.add(seqLimits);\r
1035     viewMenu.add(scaleAbove);\r
1036     viewMenu.add(scaleLeft);\r
1037     viewMenu.add(scaleRight);\r
1038     viewMenu.add(viewBoxesMenuItem);\r
1039     viewMenu.add(viewTextMenuItem);\r
1040     viewMenu.add(colourTextMenuItem);\r
1041     viewMenu.add(renderGapsMenuItem);\r
1042     viewMenu.add(annotationPanelMenuItem);\r
1043     viewMenu.addSeparator();\r
1044     viewMenu.add(fetchSeqFeatures);\r
1045     viewMenu.add(showSeqFeatures);\r
1046     viewMenu.add(featureSettings);\r
1047     viewMenu.addSeparator();\r
1048     viewMenu.add(overviewMenuItem);\r
1049     colourMenu.add(applyToAllGroups);\r
1050     colourMenu.addSeparator();\r
1051     colourMenu.add(noColourmenuItem);\r
1052     colourMenu.add(clustalColour);\r
1053     colourMenu.add(BLOSUM62Colour);\r
1054     colourMenu.add(PIDColour);\r
1055     colourMenu.add(zappoColour);\r
1056     colourMenu.add(taylorColour);\r
1057     colourMenu.add(hydrophobicityColour);\r
1058     colourMenu.add(helixColour);\r
1059     colourMenu.add(strandColour);\r
1060     colourMenu.add(turnColour);\r
1061     colourMenu.add(buriedColour);\r
1062     colourMenu.add(nucleotideColour);\r
1063     colourMenu.add(userDefinedColour);\r
1064     colourMenu.addSeparator();\r
1065     colourMenu.add(conservationMenuItem);\r
1066     colourMenu.add(modifyConservation);\r
1067     colourMenu.add(abovePIDThreshold);\r
1068     colourMenu.add(modifyPID);\r
1069     colourMenu.add(annotationColour);\r
1070     calculateMenu.add(sort);\r
1071     calculateMenu.add(calculate);\r
1072     calculateMenu.addSeparator();\r
1073     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1074     calculateMenu.add(PCAMenuItem);\r
1075     calculateMenu.addSeparator();\r
1076     calculateMenu.add(showTranslation);\r
1077     calculateMenu.add(autoCalculate);\r
1078     webServiceNoServices=new JMenuItem("<No Services>");\r
1079     webService.add(webServiceNoServices);\r
1080     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
1081   //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1082     jMenu1.add(pasteNew);\r
1083     jMenu1.add(pasteThis);\r
1084     sort.add(sortIDMenuItem);\r
1085     sort.add(sortGroupMenuItem);\r
1086     sort.add(sortPairwiseMenuItem);\r
1087     calculate.add(averageDistanceTreeMenuItem);\r
1088     calculate.add(neighbourTreeMenuItem);\r
1089     calculate.add(avDistanceTreeBlosumMenuItem);\r
1090     calculate.add(njTreeBlosumMenuItem);\r
1091     jMenu2.add(htmlMenuItem);\r
1092     jMenu2.add(epsFile);\r
1093     jMenu2.add(createPNG);\r
1094   }\r
1095 \r
1096   protected void outputText_actionPerformed(ActionEvent e)\r
1097   {\r
1098   }\r
1099 \r
1100   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1101   {\r
1102   }\r
1103 \r
1104   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1105   {\r
1106   }\r
1107 \r
1108   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1109   {\r
1110   }\r
1111 \r
1112   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1113   {\r
1114   }\r
1115 \r
1116   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1117   {\r
1118   }\r
1119 \r
1120   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1121   {\r
1122   }\r
1123 \r
1124   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1125   {\r
1126   }\r
1127 \r
1128   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1129   {\r
1130   }\r
1131 \r
1132   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1133   {\r
1134   }\r
1135 \r
1136   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1137   {\r
1138   }\r
1139 \r
1140   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1141   {\r
1142   }\r
1143 \r
1144   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1145   {\r
1146   }\r
1147 \r
1148   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1149   {\r
1150   }\r
1151 \r
1152   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1153   {\r
1154   }\r
1155 \r
1156   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1157   {\r
1158   }\r
1159 \r
1160   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1161   {\r
1162   }\r
1163 \r
1164   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1165   {\r
1166   }\r
1167 \r
1168   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1169   {\r
1170   }\r
1171 \r
1172   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1173   {\r
1174   }\r
1175 \r
1176   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1177   {\r
1178   }\r
1179 \r
1180   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1181   {\r
1182   }\r
1183 \r
1184   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1185   {\r
1186   }\r
1187 \r
1188   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1189   {\r
1190   }\r
1191 \r
1192   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1193   {\r
1194   }\r
1195 \r
1196   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1197   {\r
1198   }\r
1199 \r
1200   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1201   {\r
1202   }\r
1203 \r
1204   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1205   {\r
1206   }\r
1207 \r
1208   protected void clustalColour_actionPerformed(ActionEvent e)\r
1209   {\r
1210   }\r
1211 \r
1212   protected void zappoColour_actionPerformed(ActionEvent e)\r
1213   {\r
1214   }\r
1215 \r
1216   protected void taylorColour_actionPerformed(ActionEvent e)\r
1217   {\r
1218   }\r
1219 \r
1220   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1221   {\r
1222   }\r
1223 \r
1224   protected void helixColour_actionPerformed(ActionEvent e)\r
1225   {\r
1226   }\r
1227 \r
1228   protected void strandColour_actionPerformed(ActionEvent e)\r
1229   {\r
1230   }\r
1231 \r
1232   protected void turnColour_actionPerformed(ActionEvent e)\r
1233   {\r
1234   }\r
1235 \r
1236   protected void buriedColour_actionPerformed(ActionEvent e)\r
1237   {\r
1238   }\r
1239 \r
1240   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1241   {\r
1242   }\r
1243 \r
1244   protected void PIDColour_actionPerformed(ActionEvent e)\r
1245   {\r
1246   }\r
1247 \r
1248   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1249   {\r
1250   }\r
1251 \r
1252   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1253   {\r
1254   }\r
1255 \r
1256   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1257   {\r
1258   }\r
1259 \r
1260   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1261   {\r
1262   }\r
1263 \r
1264   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1265   {\r
1266   }\r
1267 \r
1268   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1269   {\r
1270   }\r
1271 \r
1272   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1273   {\r
1274   }\r
1275 \r
1276   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1277   {\r
1278   }\r
1279 \r
1280   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1281   {\r
1282   }\r
1283 \r
1284   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1285   {\r
1286   }\r
1287 \r
1288   protected void copy_actionPerformed(ActionEvent e)\r
1289   {\r
1290   }\r
1291 \r
1292   protected void cut_actionPerformed(ActionEvent e)\r
1293   {\r
1294   }\r
1295 \r
1296   protected void delete_actionPerformed(ActionEvent e)\r
1297   {\r
1298   }\r
1299 \r
1300   protected void pasteNew_actionPerformed(ActionEvent e)\r
1301   {\r
1302   }\r
1303 \r
1304   protected void pasteThis_actionPerformed(ActionEvent e)\r
1305   {\r
1306   }\r
1307 \r
1308   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1309   {\r
1310   }\r
1311 \r
1312   public void createPNG(java.io.File f)\r
1313   {\r
1314   }\r
1315 \r
1316   protected void font_actionPerformed(ActionEvent e)\r
1317   {\r
1318   }\r
1319 \r
1320   protected void seqLimit_actionPerformed(ActionEvent e)\r
1321   {\r
1322   }\r
1323 \r
1324   public void seqDBRef_actionPerformed(ActionEvent e)\r
1325   {\r
1326 \r
1327   }\r
1328 \r
1329 \r
1330   public void createEPS(java.io.File f)\r
1331   {\r
1332   }\r
1333 \r
1334   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1335   {\r
1336   }\r
1337 \r
1338   protected void jpred_actionPerformed(ActionEvent e)\r
1339   {\r
1340   }\r
1341 \r
1342   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1343   {\r
1344   }\r
1345 \r
1346   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1347   {\r
1348   }\r
1349 \r
1350   protected void scaleRight_actionPerformed(ActionEvent e)\r
1351   {\r
1352   }\r
1353 \r
1354   protected void modifyPID_actionPerformed(ActionEvent e)\r
1355   {\r
1356   }\r
1357 \r
1358   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1359   {\r
1360   }\r
1361 \r
1362 \r
1363 \r
1364   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1365   {\r
1366   }\r
1367 \r
1368   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1369   {\r
1370   }\r
1371 \r
1372 \r
1373   public void vamsasStore_actionPerformed(ActionEvent e)\r
1374   {\r
1375 \r
1376   }\r
1377 \r
1378   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1379   {\r
1380 \r
1381   }\r
1382 \r
1383   public void showTranslation_actionPerformed(ActionEvent e)\r
1384   {\r
1385 \r
1386   }\r
1387 \r
1388   public void featureSettings_actionPerformed(ActionEvent e)\r
1389   {\r
1390 \r
1391   }\r
1392 \r
1393   public void fetchSequence_actionPerformed(ActionEvent e)\r
1394   {\r
1395 \r
1396   }\r
1397 \r
1398   public void smoothFont_actionPerformed(ActionEvent e)\r
1399   {\r
1400 \r
1401   }\r
1402 \r
1403   public void annotationColour_actionPerformed(ActionEvent e)\r
1404   {\r
1405 \r
1406   }\r
1407 \r
1408   public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
1409   {\r
1410 \r
1411   }\r
1412 \r
1413   public void associatedData_actionPerformed(ActionEvent e)\r
1414   {\r
1415 \r
1416   }\r
1417 \r
1418   public void autoCalculate_actionPerformed(ActionEvent e)\r
1419   {\r
1420 \r
1421   }\r
1422 }\r