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