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