added help and documentation for annotation editing.
[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 import javax.swing.event.*;\r
25 \r
26 import jalview.gui.*;\r
27 import jalview.schemes.*;\r
28 \r
29 public class GAlignFrame\r
30     extends JInternalFrame\r
31 {\r
32   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
33   protected JMenu fileMenu = new JMenu();\r
34   protected JMenuItem closeMenuItem = new JMenuItem();\r
35   protected JMenu editMenu = new JMenu();\r
36   protected JMenu viewMenu = new JMenu();\r
37   protected JMenu colourMenu = new JMenu();\r
38   protected JMenu calculateMenu = new JMenu();\r
39   protected JMenu webService = new JMenu();\r
40   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
41   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
42   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
43   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
44   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
45   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
46   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
47   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
48   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
49   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
50   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
51   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
52   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
53   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
54   protected JMenuItem PCAMenuItem = new JMenuItem();\r
55   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
56   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
57   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
58   BorderLayout borderLayout1 = new BorderLayout();\r
59   public JLabel statusBar = new JLabel();\r
60   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
61   protected JMenu outputTextboxMenu = new JMenu();\r
62   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
63   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
64   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
65   protected JRadioButtonMenuItem hydrophobicityColour = new\r
66       JRadioButtonMenuItem();\r
67   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
68   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
69   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
70   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
71   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
72   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
73   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
74   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
75   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
76   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
77   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
78   JMenuItem htmlMenuItem = new JMenuItem();\r
79   JMenuItem overviewMenuItem = new JMenuItem();\r
80   protected JMenuItem undoMenuItem = new JMenuItem();\r
81   protected JMenuItem redoMenuItem = new JMenuItem();\r
82   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
83   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
84   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
85   JMenuItem printMenuItem = new JMenuItem();\r
86   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
87   JMenuItem findMenuItem = new JMenuItem();\r
88   JMenu searchMenu = new JMenu();\r
89   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
90   public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
91   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
92   JMenuItem deleteGroups = new JMenuItem();\r
93   JMenuItem delete = new JMenuItem();\r
94   JMenuItem copy = new JMenuItem();\r
95   JMenuItem cut = new JMenuItem();\r
96   JMenu jMenu1 = new JMenu();\r
97   JMenuItem pasteNew = new JMenuItem();\r
98   JMenuItem pasteThis = new JMenuItem();\r
99   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
100   JMenuItem createPNG = new JMenuItem();\r
101   protected JMenuItem font = new JMenuItem();\r
102   public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
103   JMenuItem epsFile = new JMenuItem();\r
104   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
105   JMenuItem jnet = new JMenuItem();\r
106   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
107   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
108   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
109   JMenuItem modifyPID = new JMenuItem();\r
110   JMenuItem modifyConservation = new JMenuItem();\r
111   protected JMenu sortByTreeMenu = new JMenu();\r
112   protected JMenu sort = new JMenu();\r
113   JMenu calculate = new JMenu();\r
114   JMenuItem msaAlignMenuItem = new JMenuItem();\r
115   JMenu jMenu2 = new JMenu();\r
116   JMenuItem padGapsMenuitem = new JMenuItem();\r
117   JMenuItem ClustalRealign = new JMenuItem();\r
118 \r
119   public GAlignFrame()\r
120   {\r
121     ButtonGroup colours = new ButtonGroup();\r
122     colours.add(noColourmenuItem);\r
123     colours.add(clustalColour);\r
124     colours.add(zappoColour);\r
125     colours.add(taylorColour);\r
126     colours.add(hydrophobicityColour);\r
127     colours.add(helixColour);\r
128     colours.add(strandColour);\r
129     colours.add(turnColour);\r
130     colours.add(buriedColour);\r
131     colours.add(userDefinedColour);\r
132     colours.add(PIDColour);\r
133     colours.add(BLOSUM62Colour);\r
134     colours.add(nucleotideColour);\r
135 \r
136     noColourmenuItem.setSelected(true);\r
137 \r
138     String defaultColour = Preferences.defaultColour;\r
139 \r
140     if (defaultColour != null)\r
141     {\r
142       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
143 \r
144       switch (index)\r
145       {\r
146         case ColourSchemeProperty.CLUSTAL:\r
147           clustalColour.setSelected(true);\r
148 \r
149           break;\r
150 \r
151         case ColourSchemeProperty.BLOSUM:\r
152           BLOSUM62Colour.setSelected(true);\r
153 \r
154           break;\r
155 \r
156         case ColourSchemeProperty.PID:\r
157           PIDColour.setSelected(true);\r
158 \r
159           break;\r
160 \r
161         case ColourSchemeProperty.ZAPPO:\r
162           zappoColour.setSelected(true);\r
163 \r
164           break;\r
165 \r
166         case ColourSchemeProperty.HYDROPHOBIC:\r
167           hydrophobicityColour.setSelected(true);\r
168 \r
169           break;\r
170 \r
171         case ColourSchemeProperty.HELIX:\r
172           helixColour.setSelected(true);\r
173 \r
174           break;\r
175 \r
176         case ColourSchemeProperty.STRAND:\r
177           strandColour.setSelected(true);\r
178 \r
179           break;\r
180 \r
181         case ColourSchemeProperty.TURN:\r
182           turnColour.setSelected(true);\r
183 \r
184           break;\r
185 \r
186         case ColourSchemeProperty.BURIED:\r
187           buriedColour.setSelected(true);\r
188 \r
189           break;\r
190 \r
191         case ColourSchemeProperty.NUCLEOTIDE:\r
192           nucleotideColour.setSelected(true);\r
193 \r
194           break;\r
195 \r
196         case ColourSchemeProperty.USER_DEFINED:\r
197           userDefinedColour.setSelected(true);\r
198 \r
199           break;\r
200       }\r
201     }\r
202 \r
203     try\r
204     {\r
205       jbInit();\r
206       setJMenuBar(alignFrameMenuBar);\r
207 \r
208       JMenuItem item;\r
209 \r
210       // dynamically fill save as menu with available formats\r
211       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
212       {\r
213         item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
214                              elementAt(\r
215                                  i));\r
216         item.addActionListener(new java.awt.event.ActionListener()\r
217         {\r
218           public void actionPerformed(ActionEvent e)\r
219           {\r
220             outputText_actionPerformed(e);\r
221           }\r
222         });\r
223 \r
224         outputTextboxMenu.add(item);\r
225       }\r
226     }\r
227     catch (Exception e)\r
228     {\r
229       e.printStackTrace();\r
230     }\r
231 \r
232   }\r
233 \r
234   private void jbInit()\r
235       throws Exception\r
236   {\r
237     fileMenu.setMnemonic('F');\r
238     fileMenu.setText("File");\r
239     saveAlignmentMenu.setMnemonic('L');\r
240     saveAlignmentMenu.setText("Save As");\r
241     saveAlignmentMenu.addActionListener(new ActionListener()\r
242     {\r
243       public void actionPerformed(ActionEvent e)\r
244       {\r
245         saveAlignmentMenu_actionPerformed(e);\r
246       }\r
247     });\r
248     closeMenuItem.setMnemonic('C');\r
249     closeMenuItem.setText("Close");\r
250     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
251     {\r
252       public void actionPerformed(ActionEvent e)\r
253       {\r
254         closeMenuItem_actionPerformed(e);\r
255       }\r
256     });\r
257     editMenu.setText("Edit");\r
258     viewMenu.setText("View");\r
259     colourMenu.setText("Colour");\r
260     calculateMenu.setText("Calculate");\r
261     webService.setText("Web Service");\r
262     selectAllSequenceMenuItem.setText("Select all");\r
263     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
264         java.awt.event.KeyEvent.VK_A,\r
265         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
266     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
267                                                 ActionListener()\r
268     {\r
269       public void actionPerformed(ActionEvent e)\r
270       {\r
271         selectAllSequenceMenuItem_actionPerformed(e);\r
272       }\r
273     });\r
274     deselectAllSequenceMenuItem.setText("Deselect All");\r
275     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
276                                                getKeyStroke(\r
277         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
278     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
279                                                   ActionListener()\r
280     {\r
281       public void actionPerformed(ActionEvent e)\r
282       {\r
283         deselectAllSequenceMenuItem_actionPerformed(e);\r
284       }\r
285     });\r
286     invertSequenceMenuItem.setText("Invert Selection");\r
287     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
288     {\r
289       public void actionPerformed(ActionEvent e)\r
290       {\r
291         invertSequenceMenuItem_actionPerformed(e);\r
292       }\r
293     });\r
294     remove2LeftMenuItem.setText("Remove Left");\r
295     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
296     {\r
297       public void actionPerformed(ActionEvent e)\r
298       {\r
299         remove2LeftMenuItem_actionPerformed(e);\r
300       }\r
301     });\r
302     remove2RightMenuItem.setText("Remove Right");\r
303     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
304     {\r
305       public void actionPerformed(ActionEvent e)\r
306       {\r
307         remove2RightMenuItem_actionPerformed(e);\r
308       }\r
309     });\r
310     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
311     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
312                                                  ActionListener()\r
313     {\r
314       public void actionPerformed(ActionEvent e)\r
315       {\r
316         removeGappedColumnMenuItem_actionPerformed(e);\r
317       }\r
318     });\r
319     removeAllGapsMenuItem.setText("Remove All Gaps");\r
320     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
321     {\r
322       public void actionPerformed(ActionEvent e)\r
323       {\r
324         removeAllGapsMenuItem_actionPerformed(e);\r
325       }\r
326     });\r
327     viewBoxesMenuItem.setText("Boxes");\r
328     viewBoxesMenuItem.setState(true);\r
329     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
330     {\r
331       public void actionPerformed(ActionEvent e)\r
332       {\r
333         viewBoxesMenuItem_actionPerformed(e);\r
334       }\r
335     });\r
336     viewTextMenuItem.setText("Text");\r
337     viewTextMenuItem.setState(true);\r
338     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
339     {\r
340       public void actionPerformed(ActionEvent e)\r
341       {\r
342         viewTextMenuItem_actionPerformed(e);\r
343       }\r
344     });\r
345     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
346     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
347     {\r
348       public void actionPerformed(ActionEvent e)\r
349       {\r
350         sortPairwiseMenuItem_actionPerformed(e);\r
351       }\r
352     });\r
353     sortIDMenuItem.setText("by ID");\r
354     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
355     {\r
356       public void actionPerformed(ActionEvent e)\r
357       {\r
358         sortIDMenuItem_actionPerformed(e);\r
359       }\r
360     });\r
361     sortGroupMenuItem.setText("by Group");\r
362     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
363     {\r
364       public void actionPerformed(ActionEvent e)\r
365       {\r
366         sortGroupMenuItem_actionPerformed(e);\r
367       }\r
368     });\r
369     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
370     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
371                                                ActionListener()\r
372     {\r
373       public void actionPerformed(ActionEvent e)\r
374       {\r
375         removeRedundancyMenuItem_actionPerformed(e);\r
376       }\r
377     });\r
378     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
379     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
380                                                 ActionListener()\r
381     {\r
382       public void actionPerformed(ActionEvent e)\r
383       {\r
384         pairwiseAlignmentMenuItem_actionPerformed(e);\r
385       }\r
386     });\r
387     PCAMenuItem.setText("Principal Component Analysis");\r
388     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
389     {\r
390       public void actionPerformed(ActionEvent e)\r
391       {\r
392         PCAMenuItem_actionPerformed(e);\r
393       }\r
394     });\r
395     averageDistanceTreeMenuItem.setText(\r
396         "Average Distance Using % Identity");\r
397     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
398                                                   ActionListener()\r
399     {\r
400       public void actionPerformed(ActionEvent e)\r
401       {\r
402         averageDistanceTreeMenuItem_actionPerformed(e);\r
403       }\r
404     });\r
405     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
406     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
407     {\r
408       public void actionPerformed(ActionEvent e)\r
409       {\r
410         neighbourTreeMenuItem_actionPerformed(e);\r
411       }\r
412     });\r
413     clustalAlignMenuItem.setText("Clustal Alignment");\r
414     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
415     {\r
416       public void actionPerformed(ActionEvent e)\r
417       {\r
418         clustalAlignMenuItem_actionPerformed(e);\r
419       }\r
420     });\r
421     this.getContentPane().setLayout(borderLayout1);\r
422     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
423     alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
424     {\r
425       public void ancestorAdded(AncestorEvent event)\r
426       {\r
427         alignFrameMenuBar_ancestorAdded(event);\r
428       }\r
429 \r
430       public void ancestorRemoved(AncestorEvent event)\r
431       {\r
432       }\r
433 \r
434       public void ancestorMoved(AncestorEvent event)\r
435       {\r
436       }\r
437     });\r
438     statusBar.setBackground(Color.white);\r
439     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
440     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
441     statusBar.setText("Status bar");\r
442     outputTextboxMenu.setMnemonic('T');\r
443     outputTextboxMenu.setText("Output to Textbox");\r
444     clustalColour.setText("Clustalx");\r
445 \r
446     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
447     {\r
448       public void actionPerformed(ActionEvent e)\r
449       {\r
450         clustalColour_actionPerformed(e);\r
451       }\r
452     });\r
453     zappoColour.setText("Zappo");\r
454     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
455     {\r
456       public void actionPerformed(ActionEvent e)\r
457       {\r
458         zappoColour_actionPerformed(e);\r
459       }\r
460     });\r
461     taylorColour.setText("Taylor");\r
462     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
463     {\r
464       public void actionPerformed(ActionEvent e)\r
465       {\r
466         taylorColour_actionPerformed(e);\r
467       }\r
468     });\r
469     hydrophobicityColour.setText("Hydrophobicity");\r
470     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
471     {\r
472       public void actionPerformed(ActionEvent e)\r
473       {\r
474         hydrophobicityColour_actionPerformed(e);\r
475       }\r
476     });\r
477     helixColour.setText("Helix Propensity");\r
478     helixColour.addActionListener(new java.awt.event.ActionListener()\r
479     {\r
480       public void actionPerformed(ActionEvent e)\r
481       {\r
482         helixColour_actionPerformed(e);\r
483       }\r
484     });\r
485     strandColour.setText("Strand Propensity");\r
486     strandColour.addActionListener(new java.awt.event.ActionListener()\r
487     {\r
488       public void actionPerformed(ActionEvent e)\r
489       {\r
490         strandColour_actionPerformed(e);\r
491       }\r
492     });\r
493     turnColour.setText("Turn Propensity");\r
494     turnColour.addActionListener(new java.awt.event.ActionListener()\r
495     {\r
496       public void actionPerformed(ActionEvent e)\r
497       {\r
498         turnColour_actionPerformed(e);\r
499       }\r
500     });\r
501     buriedColour.setText("Buried Index");\r
502     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
503     {\r
504       public void actionPerformed(ActionEvent e)\r
505       {\r
506         buriedColour_actionPerformed(e);\r
507       }\r
508     });\r
509     userDefinedColour.setText("User Defined...");\r
510     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
511     {\r
512       public void actionPerformed(ActionEvent e)\r
513       {\r
514         userDefinedColour_actionPerformed(e);\r
515       }\r
516     });\r
517     PIDColour.setText("Percentage Identity");\r
518     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
519     {\r
520       public void actionPerformed(ActionEvent e)\r
521       {\r
522         PIDColour_actionPerformed(e);\r
523       }\r
524     });\r
525     BLOSUM62Colour.setText("BLOSUM62 Score");\r
526     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
527     {\r
528       public void actionPerformed(ActionEvent e)\r
529       {\r
530         BLOSUM62Colour_actionPerformed(e);\r
531       }\r
532     });\r
533     avDistanceTreeBlosumMenuItem.setText(\r
534         "Average Distance Using BLOSUM62");\r
535     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
536         ActionListener()\r
537     {\r
538       public void actionPerformed(ActionEvent e)\r
539       {\r
540         avTreeBlosumMenuItem_actionPerformed(e);\r
541       }\r
542     });\r
543     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
544     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
545     {\r
546       public void actionPerformed(ActionEvent e)\r
547       {\r
548         njTreeBlosumMenuItem_actionPerformed(e);\r
549       }\r
550     });\r
551     annotationPanelMenuItem.setActionCommand("");\r
552     annotationPanelMenuItem.setText("Show Annotations");\r
553     annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
554     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
555     {\r
556       public void actionPerformed(ActionEvent e)\r
557       {\r
558         annotationPanelMenuItem_actionPerformed(e);\r
559       }\r
560     });\r
561     colourTextMenuItem.setText("Colour Text");\r
562     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
563     {\r
564       public void actionPerformed(ActionEvent e)\r
565       {\r
566         colourTextMenuItem_actionPerformed(e);\r
567       }\r
568     });\r
569     htmlMenuItem.setText("HTML");\r
570     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
571     {\r
572       public void actionPerformed(ActionEvent e)\r
573       {\r
574         htmlMenuItem_actionPerformed(e);\r
575       }\r
576     });\r
577     overviewMenuItem.setText("Overview Window");\r
578     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
579     {\r
580       public void actionPerformed(ActionEvent e)\r
581       {\r
582         overviewMenuItem_actionPerformed(e);\r
583       }\r
584     });\r
585     undoMenuItem.setEnabled(false);\r
586     undoMenuItem.setMnemonic('Z');\r
587     undoMenuItem.setText("Undo");\r
588     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
589         java.awt.event.KeyEvent.VK_Z,\r
590         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
591     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
592     {\r
593       public void actionPerformed(ActionEvent e)\r
594       {\r
595         undoMenuItem_actionPerformed(e);\r
596       }\r
597     });\r
598     redoMenuItem.setEnabled(false);\r
599     redoMenuItem.setMnemonic('0');\r
600     redoMenuItem.setText("Redo");\r
601     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
602     {\r
603       public void actionPerformed(ActionEvent e)\r
604       {\r
605         redoMenuItem_actionPerformed(e);\r
606       }\r
607     });\r
608     conservationMenuItem.setText("By Conservation");\r
609     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
610     {\r
611       public void actionPerformed(ActionEvent e)\r
612       {\r
613         conservationMenuItem_actionPerformed(e);\r
614       }\r
615     });\r
616     noColourmenuItem.setText("None");\r
617     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
618     {\r
619       public void actionPerformed(ActionEvent e)\r
620       {\r
621         noColourmenuItem_actionPerformed(e);\r
622       }\r
623     });\r
624     wrapMenuItem.setText("Wrap");\r
625     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
626     {\r
627       public void actionPerformed(ActionEvent e)\r
628       {\r
629         wrapMenuItem_actionPerformed(e);\r
630       }\r
631     });\r
632     printMenuItem.setText("Print");\r
633     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
634     {\r
635       public void actionPerformed(ActionEvent e)\r
636       {\r
637         printMenuItem_actionPerformed(e);\r
638       }\r
639     });\r
640     renderGapsMenuItem.setText("Show Gaps");\r
641     renderGapsMenuItem.setState(true);\r
642     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
643     {\r
644       public void actionPerformed(ActionEvent e)\r
645       {\r
646         renderGapsMenuItem_actionPerformed(e);\r
647       }\r
648     });\r
649     findMenuItem.setText("Find...");\r
650     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
651         java.awt.event.KeyEvent.VK_F,\r
652         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
653     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
654     {\r
655       public void actionPerformed(ActionEvent e)\r
656       {\r
657         findMenuItem_actionPerformed(e);\r
658       }\r
659     });\r
660     searchMenu.setText("Search");\r
661 \r
662     abovePIDThreshold.setText("Above Identity Threshold");\r
663     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
664     {\r
665       public void actionPerformed(ActionEvent e)\r
666       {\r
667         abovePIDThreshold_actionPerformed(e);\r
668       }\r
669     });\r
670     sequenceFeatures.setText("Sequence Features");\r
671     sequenceFeatures.addActionListener(new ActionListener()\r
672     {\r
673       public void actionPerformed(ActionEvent actionEvent)\r
674       {\r
675         sequenceFeatures_actionPerformed(actionEvent);\r
676       }\r
677     });\r
678     nucleotideColour.setText("Nucleotide");\r
679     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
680     {\r
681       public void actionPerformed(ActionEvent e)\r
682       {\r
683         nucleotideColour_actionPerformed(e);\r
684       }\r
685     });\r
686     deleteGroups.setText("Undefine groups");\r
687     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
688     {\r
689       public void actionPerformed(ActionEvent e)\r
690       {\r
691         deleteGroups_actionPerformed(e);\r
692       }\r
693     });\r
694     copy.setText("Copy");\r
695     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
696         java.awt.event.KeyEvent.VK_C,\r
697         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
698     copy.setMnemonic(KeyEvent.VK_C);\r
699 \r
700     copy.addActionListener(new java.awt.event.ActionListener()\r
701     {\r
702       public void actionPerformed(ActionEvent e)\r
703       {\r
704         copy_actionPerformed(e);\r
705       }\r
706     });\r
707     cut.setText("Cut");\r
708     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
709         java.awt.event.KeyEvent.VK_X,\r
710         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
711     cut.setMnemonic(KeyEvent.VK_X);\r
712     cut.addActionListener(new java.awt.event.ActionListener()\r
713     {\r
714       public void actionPerformed(ActionEvent e)\r
715       {\r
716         cut_actionPerformed(e);\r
717       }\r
718     });\r
719     delete.setText("Delete");\r
720     delete.addActionListener(new java.awt.event.ActionListener()\r
721     {\r
722       public void actionPerformed(ActionEvent e)\r
723       {\r
724         delete_actionPerformed(e);\r
725       }\r
726     });\r
727     jMenu1.setMnemonic('V');\r
728     jMenu1.setText("Paste");\r
729     pasteNew.setText("To New Alignment");\r
730     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
731         java.awt.event.KeyEvent.VK_V,\r
732         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
733     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
734     {\r
735       public void actionPerformed(ActionEvent e)\r
736       {\r
737         pasteNew_actionPerformed(e);\r
738       }\r
739     });\r
740     pasteThis.setText("Add To This Alignment");\r
741     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
742     {\r
743       public void actionPerformed(ActionEvent e)\r
744       {\r
745         pasteThis_actionPerformed(e);\r
746       }\r
747     });\r
748     applyToAllGroups.setText("Apply Colour To All Groups");\r
749     applyToAllGroups.setState(true);\r
750     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
751     {\r
752       public void actionPerformed(ActionEvent e)\r
753       {\r
754         applyToAllGroups_actionPerformed(e);\r
755       }\r
756     });\r
757     createPNG.addActionListener(new java.awt.event.ActionListener()\r
758     {\r
759       public void actionPerformed(ActionEvent e)\r
760       {\r
761         createPNG(null);\r
762       }\r
763     });\r
764     createPNG.setActionCommand("Save As PNG Image");\r
765     createPNG.setText("PNG");\r
766     font.setText("Font...");\r
767     font.addActionListener(new java.awt.event.ActionListener()\r
768     {\r
769       public void actionPerformed(ActionEvent e)\r
770       {\r
771         font_actionPerformed(e);\r
772       }\r
773     });\r
774     fullSeqId.setText("Show Full Sequence ID");\r
775     fullSeqId.setState(true);\r
776     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
777     {\r
778       public void actionPerformed(ActionEvent e)\r
779       {\r
780         fullSeqId_actionPerformed(e);\r
781       }\r
782     });\r
783     epsFile.setText("EPS");\r
784     epsFile.addActionListener(new java.awt.event.ActionListener()\r
785     {\r
786       public void actionPerformed(ActionEvent e)\r
787       {\r
788         createEPS(null);\r
789       }\r
790     });\r
791     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
792     LoadtreeMenuItem.setText("Load Assocated Tree");\r
793     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
794     {\r
795       public void actionPerformed(ActionEvent e)\r
796       {\r
797         LoadtreeMenuItem_actionPerformed(e);\r
798       }\r
799     });\r
800     jnet.setText("JNet");\r
801     jnet.addActionListener(new java.awt.event.ActionListener()\r
802     {\r
803       public void actionPerformed(ActionEvent e)\r
804       {\r
805         jpred_actionPerformed(e);\r
806       }\r
807     });\r
808     scaleAbove.setVisible(false);\r
809     scaleAbove.setText("Scale Above");\r
810     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
811     {\r
812       public void actionPerformed(ActionEvent e)\r
813       {\r
814         scaleAbove_actionPerformed(e);\r
815       }\r
816     });\r
817     scaleLeft.setVisible(false);\r
818     scaleLeft.setSelected(true);\r
819     scaleLeft.setText("Scale Left");\r
820     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
821     {\r
822       public void actionPerformed(ActionEvent e)\r
823       {\r
824         scaleLeft_actionPerformed(e);\r
825       }\r
826     });\r
827     scaleRight.setVisible(false);\r
828     scaleRight.setSelected(true);\r
829     scaleRight.setText("Scale Right");\r
830     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
831     {\r
832       public void actionPerformed(ActionEvent e)\r
833       {\r
834         scaleRight_actionPerformed(e);\r
835       }\r
836     });\r
837     modifyPID.setText("Modify Identity Threshold...");\r
838     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
839     {\r
840       public void actionPerformed(ActionEvent e)\r
841       {\r
842         modifyPID_actionPerformed(e);\r
843       }\r
844     });\r
845     modifyConservation.setText("Modify Conservation Threshold...");\r
846     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
847     {\r
848       public void actionPerformed(ActionEvent e)\r
849       {\r
850         modifyConservation_actionPerformed(e);\r
851       }\r
852     });\r
853     sortByTreeMenu.setText("By Tree Order");\r
854     sort.setText("Sort");\r
855     calculate.setText("Calculate Tree");\r
856     msaAlignMenuItem.setText("Muscle Alignment");\r
857     msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
858     {\r
859       public void actionPerformed(ActionEvent e)\r
860       {\r
861         msaAlignMenuItem_actionPerformed(e);\r
862       }\r
863     });\r
864     jMenu2.setText("Export");\r
865     padGapsMenuitem.setText("Pad Gaps");\r
866     padGapsMenuitem.addActionListener(new ActionListener()\r
867     {\r
868       public void actionPerformed(ActionEvent e)\r
869       {\r
870         padGapsMenuitem_actionPerformed(e);\r
871       }\r
872     });\r
873     ClustalRealign.setText("Clustal Realign");\r
874     ClustalRealign.addActionListener(new ActionListener()\r
875     {\r
876       public void actionPerformed(ActionEvent e)\r
877       {\r
878         ClustalRealign_actionPerformed(e);\r
879       }\r
880     });\r
881     alignFrameMenuBar.add(fileMenu);\r
882     alignFrameMenuBar.add(editMenu);\r
883     alignFrameMenuBar.add(searchMenu);\r
884     alignFrameMenuBar.add(viewMenu);\r
885     alignFrameMenuBar.add(colourMenu);\r
886     alignFrameMenuBar.add(calculateMenu);\r
887     fileMenu.add(saveAlignmentMenu);\r
888     fileMenu.add(jMenu2);\r
889     fileMenu.add(outputTextboxMenu);\r
890     fileMenu.add(printMenuItem);\r
891     fileMenu.addSeparator();\r
892     fileMenu.add(LoadtreeMenuItem);\r
893     fileMenu.addSeparator();\r
894     fileMenu.add(closeMenuItem);\r
895     editMenu.add(undoMenuItem);\r
896     editMenu.add(redoMenuItem);\r
897     editMenu.add(cut);\r
898     editMenu.add(copy);\r
899     editMenu.add(jMenu1);\r
900     editMenu.add(delete);\r
901     editMenu.addSeparator();\r
902     editMenu.add(selectAllSequenceMenuItem);\r
903     editMenu.add(deselectAllSequenceMenuItem);\r
904     editMenu.add(invertSequenceMenuItem);\r
905     editMenu.add(deleteGroups);\r
906     editMenu.addSeparator();\r
907     editMenu.add(remove2LeftMenuItem);\r
908     editMenu.add(remove2RightMenuItem);\r
909     editMenu.add(removeGappedColumnMenuItem);\r
910     editMenu.add(removeAllGapsMenuItem);\r
911     editMenu.add(removeRedundancyMenuItem);\r
912     editMenu.addSeparator();\r
913     editMenu.add(padGapsMenuitem);\r
914     searchMenu.add(findMenuItem);\r
915     viewMenu.add(font);\r
916     viewMenu.addSeparator();\r
917     viewMenu.add(wrapMenuItem);\r
918     viewMenu.add(fullSeqId);\r
919     viewMenu.add(scaleAbove);\r
920     viewMenu.add(scaleLeft);\r
921     viewMenu.add(scaleRight);\r
922     viewMenu.add(viewBoxesMenuItem);\r
923     viewMenu.add(viewTextMenuItem);\r
924     viewMenu.add(colourTextMenuItem);\r
925     viewMenu.add(renderGapsMenuItem);\r
926     viewMenu.add(annotationPanelMenuItem);\r
927     viewMenu.add(sequenceFeatures);\r
928     viewMenu.addSeparator();\r
929     viewMenu.add(overviewMenuItem);\r
930     colourMenu.add(applyToAllGroups);\r
931     colourMenu.addSeparator();\r
932     colourMenu.add(noColourmenuItem);\r
933     colourMenu.add(clustalColour);\r
934     colourMenu.add(BLOSUM62Colour);\r
935     colourMenu.add(PIDColour);\r
936     colourMenu.add(zappoColour);\r
937     colourMenu.add(taylorColour);\r
938     colourMenu.add(hydrophobicityColour);\r
939     colourMenu.add(helixColour);\r
940     colourMenu.add(strandColour);\r
941     colourMenu.add(turnColour);\r
942     colourMenu.add(buriedColour);\r
943     colourMenu.add(nucleotideColour);\r
944     colourMenu.add(userDefinedColour);\r
945     colourMenu.addSeparator();\r
946     colourMenu.add(conservationMenuItem);\r
947     colourMenu.add(modifyConservation);\r
948     colourMenu.add(abovePIDThreshold);\r
949     colourMenu.add(modifyPID);\r
950     calculateMenu.add(sort);\r
951     calculateMenu.add(calculate);\r
952     calculateMenu.addSeparator();\r
953     calculateMenu.add(pairwiseAlignmentMenuItem);\r
954     calculateMenu.add(PCAMenuItem);\r
955     calculateMenu.addSeparator();\r
956     calculateMenu.add(webService);\r
957     webService.add(clustalAlignMenuItem);\r
958     webService.add(msaAlignMenuItem);\r
959     webService.add(jnet);\r
960     webService.add(ClustalRealign);\r
961     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
962     jMenu1.add(pasteNew);\r
963     jMenu1.add(pasteThis);\r
964     sort.add(sortIDMenuItem);\r
965     sort.add(sortGroupMenuItem);\r
966     sort.add(sortPairwiseMenuItem);\r
967     calculate.add(averageDistanceTreeMenuItem);\r
968     calculate.add(neighbourTreeMenuItem);\r
969     calculate.add(avDistanceTreeBlosumMenuItem);\r
970     calculate.add(njTreeBlosumMenuItem);\r
971     jMenu2.add(htmlMenuItem);\r
972     jMenu2.add(epsFile);\r
973     jMenu2.add(createPNG);\r
974   }\r
975 \r
976   protected void outputText_actionPerformed(ActionEvent e)\r
977   {\r
978   }\r
979 \r
980   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
981   {\r
982   }\r
983 \r
984   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
985   {\r
986   }\r
987 \r
988   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
989   {\r
990   }\r
991 \r
992   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
993   {\r
994   }\r
995 \r
996   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
997   {\r
998   }\r
999 \r
1000   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1001   {\r
1002   }\r
1003 \r
1004   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1005   {\r
1006   }\r
1007 \r
1008   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1009   {\r
1010   }\r
1011 \r
1012   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1013   {\r
1014   }\r
1015 \r
1016   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1017   {\r
1018   }\r
1019 \r
1020   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1021   {\r
1022   }\r
1023 \r
1024   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1025   {\r
1026   }\r
1027 \r
1028   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1029   {\r
1030   }\r
1031 \r
1032   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1033   {\r
1034   }\r
1035 \r
1036   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1037   {\r
1038   }\r
1039 \r
1040   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1041   {\r
1042   }\r
1043 \r
1044   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1045   {\r
1046   }\r
1047 \r
1048   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1049   {\r
1050   }\r
1051 \r
1052   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1053   {\r
1054   }\r
1055 \r
1056   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1057   {\r
1058   }\r
1059 \r
1060   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1061   {\r
1062   }\r
1063 \r
1064   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1065   {\r
1066   }\r
1067 \r
1068   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1069   {\r
1070   }\r
1071 \r
1072   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1073   {\r
1074   }\r
1075 \r
1076   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1077   {\r
1078   }\r
1079 \r
1080   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1081   {\r
1082   }\r
1083 \r
1084   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1085   {\r
1086   }\r
1087 \r
1088   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1089   {\r
1090   }\r
1091 \r
1092   protected void clustalColour_actionPerformed(ActionEvent e)\r
1093   {\r
1094   }\r
1095 \r
1096   protected void zappoColour_actionPerformed(ActionEvent e)\r
1097   {\r
1098   }\r
1099 \r
1100   protected void taylorColour_actionPerformed(ActionEvent e)\r
1101   {\r
1102   }\r
1103 \r
1104   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1105   {\r
1106   }\r
1107 \r
1108   protected void helixColour_actionPerformed(ActionEvent e)\r
1109   {\r
1110   }\r
1111 \r
1112   protected void strandColour_actionPerformed(ActionEvent e)\r
1113   {\r
1114   }\r
1115 \r
1116   protected void turnColour_actionPerformed(ActionEvent e)\r
1117   {\r
1118   }\r
1119 \r
1120   protected void buriedColour_actionPerformed(ActionEvent e)\r
1121   {\r
1122   }\r
1123 \r
1124   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1125   {\r
1126   }\r
1127 \r
1128   protected void PIDColour_actionPerformed(ActionEvent e)\r
1129   {\r
1130   }\r
1131 \r
1132   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1133   {\r
1134   }\r
1135 \r
1136   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1137   {\r
1138   }\r
1139 \r
1140   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1141   {\r
1142   }\r
1143 \r
1144   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1145   {\r
1146   }\r
1147 \r
1148   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1149   {\r
1150   }\r
1151 \r
1152   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1153   {\r
1154   }\r
1155 \r
1156   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1157   {\r
1158   }\r
1159 \r
1160   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1161   {\r
1162   }\r
1163 \r
1164   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1165   {\r
1166   }\r
1167 \r
1168   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1169   {\r
1170   }\r
1171 \r
1172   protected void copy_actionPerformed(ActionEvent e)\r
1173   {\r
1174   }\r
1175 \r
1176   protected void cut_actionPerformed(ActionEvent e)\r
1177   {\r
1178   }\r
1179 \r
1180   protected void delete_actionPerformed(ActionEvent e)\r
1181   {\r
1182   }\r
1183 \r
1184   protected void pasteNew_actionPerformed(ActionEvent e)\r
1185   {\r
1186   }\r
1187 \r
1188   protected void pasteThis_actionPerformed(ActionEvent e)\r
1189   {\r
1190   }\r
1191 \r
1192   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1193   {\r
1194   }\r
1195 \r
1196   public void createPNG(java.io.File f)\r
1197   {\r
1198   }\r
1199 \r
1200   protected void font_actionPerformed(ActionEvent e)\r
1201   {\r
1202   }\r
1203 \r
1204   protected void fullSeqId_actionPerformed(ActionEvent e)\r
1205   {\r
1206   }\r
1207 \r
1208   public void createEPS(java.io.File f)\r
1209   {\r
1210   }\r
1211 \r
1212   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1213   {\r
1214   }\r
1215 \r
1216   protected void jpred_actionPerformed(ActionEvent e)\r
1217   {\r
1218   }\r
1219 \r
1220   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1221   {\r
1222   }\r
1223 \r
1224   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1225   {\r
1226   }\r
1227 \r
1228   protected void scaleRight_actionPerformed(ActionEvent e)\r
1229   {\r
1230   }\r
1231 \r
1232   protected void modifyPID_actionPerformed(ActionEvent e)\r
1233   {\r
1234   }\r
1235 \r
1236   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1237   {\r
1238   }\r
1239 \r
1240   protected void preferences_actionPerformed(ActionEvent e)\r
1241   {\r
1242   }\r
1243 \r
1244   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1245   {\r
1246   }\r
1247 \r
1248   protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
1249   {\r
1250   }\r
1251 \r
1252   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1253   {\r
1254   }\r
1255 \r
1256   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1257   {\r
1258   }\r
1259 \r
1260   protected void ClustalRealign_actionPerformed(ActionEvent e)\r
1261   {\r
1262   }\r
1263 }\r