Put DBRefFether in a new thread
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
1 /*\r
2  * Jalview - A Sequence Alignment Editor and Viewer\r
3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
4  *\r
5  * This program is free software; you can redistribute it and/or\r
6  * modify it under the terms of the GNU General Public License\r
7  * as published by the Free Software Foundation; either version 2\r
8  * of the License, or (at your option) any later version.\r
9  *\r
10  * This program is distributed in the hope that it will be useful,\r
11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
13  * GNU General Public License for more details.\r
14  *\r
15  * You should have received a copy of the GNU General Public License\r
16  * along with this program; if not, write to the Free Software\r
17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
18  */\r
19 package jalview.jbgui;\r
20 \r
21 import java.awt.*;\r
22 import java.awt.event.*;\r
23 import javax.swing.*;\r
24 \r
25 import jalview.schemes.*;\r
26 import java.awt.BorderLayout;\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 showSeqFeatures = 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   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
115   protected ButtonGroup colours = new ButtonGroup();\r
116   JMenuItem vamsasStore = new JMenuItem();\r
117   protected JMenuItem showTranslation = new JMenuItem();\r
118   public JMenuItem featureSettings = new JMenuItem();\r
119   JMenuItem fetchSequence = new JMenuItem();\r
120   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
121   JMenuItem annotationColour = new JMenuItem();\r
122   JMenuItem associatedData = new JMenuItem();\r
123   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
124   JMenu addSequenceMenu = new JMenu();\r
125   JMenuItem addFromFile = new JMenuItem();\r
126   JMenuItem addFromText = new JMenuItem();\r
127   JMenuItem addFromURL = new JMenuItem();\r
128   JMenuItem exportAnnotations = new JMenuItem();\r
129   JMenuItem exportFeatures = new JMenuItem();\r
130   protected JPanel statusPanel = new JPanel();\r
131   GridLayout gridLayout1 = new GridLayout();\r
132   JMenu jMenu3 = new JMenu();\r
133   JMenuItem showAllSeqs = new JMenuItem();\r
134   JMenuItem showAllColumns = new JMenuItem();\r
135   JMenu jMenu4 = new JMenu();\r
136   JMenuItem hideSelSequences = new JMenuItem();\r
137   JMenuItem hideSelColumns = new JMenuItem();\r
138   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
139   public GAlignFrame()\r
140   {\r
141 \r
142 \r
143     try\r
144     {\r
145       jbInit();\r
146       setJMenuBar(alignFrameMenuBar);\r
147 \r
148       // dynamically fill save as menu with available formats\r
149       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
150       {\r
151         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
152                              elementAt(\r
153                                  i));\r
154         item.addActionListener(new java.awt.event.ActionListener()\r
155         {\r
156           public void actionPerformed(ActionEvent e)\r
157           {\r
158             outputText_actionPerformed(e);\r
159           }\r
160         });\r
161 \r
162         outputTextboxMenu.add(item);\r
163       }\r
164     }\r
165     catch (Exception e)\r
166     {\r
167     }\r
168 \r
169 \r
170     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
171     {\r
172       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
173           getUserColourSchemes().keys();\r
174 \r
175       while (userColours.hasMoreElements())\r
176       {\r
177         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
178             nextElement().toString());\r
179         radioItem.setName("USER_DEFINED");\r
180         radioItem.addMouseListener(new MouseAdapter()\r
181             {\r
182               public void mousePressed(MouseEvent evt)\r
183               {\r
184                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
185                 {\r
186                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
187 \r
188                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
189                       "Remove from default list?",\r
190                       "Remove user defined colour",\r
191                       JOptionPane.YES_NO_OPTION);\r
192                   if(option == JOptionPane.YES_OPTION)\r
193                   {\r
194                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
195                     colourMenu.remove(radioItem);\r
196                   }\r
197                   else\r
198                     radioItem.addActionListener(new ActionListener()\r
199                     {\r
200                       public void actionPerformed(ActionEvent evt)\r
201                       {\r
202                         userDefinedColour_actionPerformed(evt);\r
203                       }\r
204                     });\r
205                 }\r
206               }\r
207             });\r
208         radioItem.addActionListener(new ActionListener()\r
209         {\r
210           public void actionPerformed(ActionEvent evt)\r
211           {\r
212             userDefinedColour_actionPerformed(evt);\r
213           }\r
214         });\r
215         colourMenu.insert(radioItem, 15);\r
216         colours.add(radioItem);\r
217       }\r
218     }\r
219     colours.add(noColourmenuItem);\r
220     colours.add(clustalColour);\r
221     colours.add(zappoColour);\r
222     colours.add(taylorColour);\r
223     colours.add(hydrophobicityColour);\r
224     colours.add(helixColour);\r
225     colours.add(strandColour);\r
226     colours.add(turnColour);\r
227     colours.add(buriedColour);\r
228     colours.add(userDefinedColour);\r
229     colours.add(PIDColour);\r
230     colours.add(BLOSUM62Colour);\r
231     colours.add(nucleotideColour);\r
232 \r
233     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
234 \r
235 \r
236   }\r
237 \r
238   public void setColourSelected(String defaultColour)\r
239   {\r
240 \r
241     if (defaultColour != null)\r
242     {\r
243       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
244 \r
245       switch (index)\r
246       {\r
247         case ColourSchemeProperty.NONE:\r
248               noColourmenuItem.setSelected(true);\r
249               break;\r
250         case ColourSchemeProperty.CLUSTAL:\r
251           clustalColour.setSelected(true);\r
252 \r
253           break;\r
254 \r
255         case ColourSchemeProperty.BLOSUM:\r
256           BLOSUM62Colour.setSelected(true);\r
257 \r
258           break;\r
259 \r
260         case ColourSchemeProperty.PID:\r
261           PIDColour.setSelected(true);\r
262 \r
263           break;\r
264 \r
265         case ColourSchemeProperty.ZAPPO:\r
266           zappoColour.setSelected(true);\r
267 \r
268           break;\r
269 \r
270         case ColourSchemeProperty.TAYLOR:\r
271           taylorColour.setSelected(true);\r
272           break;\r
273 \r
274         case ColourSchemeProperty.HYDROPHOBIC:\r
275           hydrophobicityColour.setSelected(true);\r
276 \r
277           break;\r
278 \r
279         case ColourSchemeProperty.HELIX:\r
280           helixColour.setSelected(true);\r
281 \r
282           break;\r
283 \r
284         case ColourSchemeProperty.STRAND:\r
285           strandColour.setSelected(true);\r
286 \r
287           break;\r
288 \r
289         case ColourSchemeProperty.TURN:\r
290           turnColour.setSelected(true);\r
291 \r
292           break;\r
293 \r
294         case ColourSchemeProperty.BURIED:\r
295           buriedColour.setSelected(true);\r
296 \r
297           break;\r
298 \r
299         case ColourSchemeProperty.NUCLEOTIDE:\r
300           nucleotideColour.setSelected(true);\r
301 \r
302           break;\r
303 \r
304         case ColourSchemeProperty.USER_DEFINED:\r
305           userDefinedColour.setSelected(true);\r
306 \r
307           break;\r
308       }\r
309     }\r
310 \r
311   }\r
312 \r
313   private void jbInit()\r
314       throws Exception\r
315   {\r
316     fileMenu.setMnemonic('F');\r
317     fileMenu.setText("File");\r
318     saveAlignmentMenu.setMnemonic('L');\r
319     saveAlignmentMenu.setText("Save As");\r
320     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
321         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
322     saveAlignmentMenu.addActionListener(new ActionListener()\r
323     {\r
324       public void actionPerformed(ActionEvent e)\r
325       {\r
326         saveAlignmentMenu_actionPerformed(e);\r
327       }\r
328     });\r
329     closeMenuItem.setMnemonic('C');\r
330     closeMenuItem.setText("Close");\r
331     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
332     {\r
333       public void actionPerformed(ActionEvent e)\r
334       {\r
335         closeMenuItem_actionPerformed(e);\r
336       }\r
337     });\r
338     editMenu.setText("Edit");\r
339     viewMenu.setText("View");\r
340     colourMenu.setText("Colour");\r
341     calculateMenu.setText("Calculate");\r
342     webService.setText("Web Service");\r
343     selectAllSequenceMenuItem.setText("Select all");\r
344     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
345         java.awt.event.KeyEvent.VK_A,\r
346         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
347     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
348                                                 ActionListener()\r
349     {\r
350       public void actionPerformed(ActionEvent e)\r
351       {\r
352         selectAllSequenceMenuItem_actionPerformed(e);\r
353       }\r
354     });\r
355     deselectAllSequenceMenuItem.setText("Deselect All");\r
356     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
357                                                getKeyStroke(\r
358         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
359     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
360                                                   ActionListener()\r
361     {\r
362       public void actionPerformed(ActionEvent e)\r
363       {\r
364         deselectAllSequenceMenuItem_actionPerformed(e);\r
365       }\r
366     });\r
367     invertSequenceMenuItem.setText("Invert Selection");\r
368     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
369     {\r
370       public void actionPerformed(ActionEvent e)\r
371       {\r
372         invertSequenceMenuItem_actionPerformed(e);\r
373       }\r
374     });\r
375     remove2LeftMenuItem.setText("Remove Left");\r
376     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
377     {\r
378       public void actionPerformed(ActionEvent e)\r
379       {\r
380         remove2LeftMenuItem_actionPerformed(e);\r
381       }\r
382     });\r
383     remove2RightMenuItem.setText("Remove Right");\r
384     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
385     {\r
386       public void actionPerformed(ActionEvent e)\r
387       {\r
388         remove2RightMenuItem_actionPerformed(e);\r
389       }\r
390     });\r
391     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
392     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
393                                                  ActionListener()\r
394     {\r
395       public void actionPerformed(ActionEvent e)\r
396       {\r
397         removeGappedColumnMenuItem_actionPerformed(e);\r
398       }\r
399     });\r
400     removeAllGapsMenuItem.setText("Remove All Gaps");\r
401     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
402     {\r
403       public void actionPerformed(ActionEvent e)\r
404       {\r
405         removeAllGapsMenuItem_actionPerformed(e);\r
406       }\r
407     });\r
408     viewBoxesMenuItem.setText("Boxes");\r
409     viewBoxesMenuItem.setState(true);\r
410     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
411     {\r
412       public void actionPerformed(ActionEvent e)\r
413       {\r
414         viewBoxesMenuItem_actionPerformed(e);\r
415       }\r
416     });\r
417     viewTextMenuItem.setText("Text");\r
418     viewTextMenuItem.setState(true);\r
419     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
420     {\r
421       public void actionPerformed(ActionEvent e)\r
422       {\r
423         viewTextMenuItem_actionPerformed(e);\r
424       }\r
425     });\r
426     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
427     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
428     {\r
429       public void actionPerformed(ActionEvent e)\r
430       {\r
431         sortPairwiseMenuItem_actionPerformed(e);\r
432       }\r
433     });\r
434     sortIDMenuItem.setText("by ID");\r
435     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
436     {\r
437       public void actionPerformed(ActionEvent e)\r
438       {\r
439         sortIDMenuItem_actionPerformed(e);\r
440       }\r
441     });\r
442     sortGroupMenuItem.setText("by Group");\r
443     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
444     {\r
445       public void actionPerformed(ActionEvent e)\r
446       {\r
447         sortGroupMenuItem_actionPerformed(e);\r
448       }\r
449     });\r
450     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
451     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
452                                                ActionListener()\r
453     {\r
454       public void actionPerformed(ActionEvent e)\r
455       {\r
456         removeRedundancyMenuItem_actionPerformed(e);\r
457       }\r
458     });\r
459     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
460     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
461                                                 ActionListener()\r
462     {\r
463       public void actionPerformed(ActionEvent e)\r
464       {\r
465         pairwiseAlignmentMenuItem_actionPerformed(e);\r
466       }\r
467     });\r
468     PCAMenuItem.setText("Principal Component Analysis");\r
469     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
470     {\r
471       public void actionPerformed(ActionEvent e)\r
472       {\r
473         PCAMenuItem_actionPerformed(e);\r
474       }\r
475     });\r
476     averageDistanceTreeMenuItem.setText(\r
477         "Average Distance Using % Identity");\r
478     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
479                                                   ActionListener()\r
480     {\r
481       public void actionPerformed(ActionEvent e)\r
482       {\r
483         averageDistanceTreeMenuItem_actionPerformed(e);\r
484       }\r
485     });\r
486     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
487     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
488     {\r
489       public void actionPerformed(ActionEvent e)\r
490       {\r
491         neighbourTreeMenuItem_actionPerformed(e);\r
492       }\r
493     });\r
494     this.getContentPane().setLayout(borderLayout1);\r
495     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
496     statusBar.setBackground(Color.white);\r
497     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
498     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
499     statusBar.setText("Status bar");\r
500     outputTextboxMenu.setMnemonic('T');\r
501     outputTextboxMenu.setText("Output to Textbox");\r
502     clustalColour.setText("Clustalx");\r
503 \r
504     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
505     {\r
506       public void actionPerformed(ActionEvent e)\r
507       {\r
508         clustalColour_actionPerformed(e);\r
509       }\r
510     });\r
511     zappoColour.setText("Zappo");\r
512     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
513     {\r
514       public void actionPerformed(ActionEvent e)\r
515       {\r
516         zappoColour_actionPerformed(e);\r
517       }\r
518     });\r
519     taylorColour.setText("Taylor");\r
520     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
521     {\r
522       public void actionPerformed(ActionEvent e)\r
523       {\r
524         taylorColour_actionPerformed(e);\r
525       }\r
526     });\r
527     hydrophobicityColour.setText("Hydrophobicity");\r
528     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
529     {\r
530       public void actionPerformed(ActionEvent e)\r
531       {\r
532         hydrophobicityColour_actionPerformed(e);\r
533       }\r
534     });\r
535     helixColour.setText("Helix Propensity");\r
536     helixColour.addActionListener(new java.awt.event.ActionListener()\r
537     {\r
538       public void actionPerformed(ActionEvent e)\r
539       {\r
540         helixColour_actionPerformed(e);\r
541       }\r
542     });\r
543     strandColour.setText("Strand Propensity");\r
544     strandColour.addActionListener(new java.awt.event.ActionListener()\r
545     {\r
546       public void actionPerformed(ActionEvent e)\r
547       {\r
548         strandColour_actionPerformed(e);\r
549       }\r
550     });\r
551     turnColour.setText("Turn Propensity");\r
552     turnColour.addActionListener(new java.awt.event.ActionListener()\r
553     {\r
554       public void actionPerformed(ActionEvent e)\r
555       {\r
556         turnColour_actionPerformed(e);\r
557       }\r
558     });\r
559     buriedColour.setText("Buried Index");\r
560     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
561     {\r
562       public void actionPerformed(ActionEvent e)\r
563       {\r
564         buriedColour_actionPerformed(e);\r
565       }\r
566     });\r
567     userDefinedColour.setText("User Defined...");\r
568     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
569     {\r
570       public void actionPerformed(ActionEvent e)\r
571       {\r
572         userDefinedColour_actionPerformed(e);\r
573       }\r
574     });\r
575     PIDColour.setText("Percentage Identity");\r
576     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
577     {\r
578       public void actionPerformed(ActionEvent e)\r
579       {\r
580         PIDColour_actionPerformed(e);\r
581       }\r
582     });\r
583     BLOSUM62Colour.setText("BLOSUM62 Score");\r
584     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
585     {\r
586       public void actionPerformed(ActionEvent e)\r
587       {\r
588         BLOSUM62Colour_actionPerformed(e);\r
589       }\r
590     });\r
591     avDistanceTreeBlosumMenuItem.setText(\r
592         "Average Distance Using BLOSUM62");\r
593     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
594         ActionListener()\r
595     {\r
596       public void actionPerformed(ActionEvent e)\r
597       {\r
598         avTreeBlosumMenuItem_actionPerformed(e);\r
599       }\r
600     });\r
601     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
602     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
603     {\r
604       public void actionPerformed(ActionEvent e)\r
605       {\r
606         njTreeBlosumMenuItem_actionPerformed(e);\r
607       }\r
608     });\r
609     annotationPanelMenuItem.setActionCommand("");\r
610     annotationPanelMenuItem.setText("Show Annotations");\r
611     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
612     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
613     {\r
614       public void actionPerformed(ActionEvent e)\r
615       {\r
616         annotationPanelMenuItem_actionPerformed(e);\r
617       }\r
618     });\r
619     colourTextMenuItem.setText("Colour Text");\r
620     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
621     {\r
622       public void actionPerformed(ActionEvent e)\r
623       {\r
624         colourTextMenuItem_actionPerformed(e);\r
625       }\r
626     });\r
627     htmlMenuItem.setText("HTML");\r
628     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
629     {\r
630       public void actionPerformed(ActionEvent e)\r
631       {\r
632         htmlMenuItem_actionPerformed(e);\r
633       }\r
634     });\r
635     overviewMenuItem.setText("Overview Window");\r
636     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
637     {\r
638       public void actionPerformed(ActionEvent e)\r
639       {\r
640         overviewMenuItem_actionPerformed(e);\r
641       }\r
642     });\r
643     undoMenuItem.setEnabled(false);\r
644     undoMenuItem.setMnemonic('Z');\r
645     undoMenuItem.setText("Undo");\r
646     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
647         java.awt.event.KeyEvent.VK_Z,\r
648         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
649     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
650     {\r
651       public void actionPerformed(ActionEvent e)\r
652       {\r
653         undoMenuItem_actionPerformed(e);\r
654       }\r
655     });\r
656     redoMenuItem.setEnabled(false);\r
657     redoMenuItem.setMnemonic('0');\r
658     redoMenuItem.setText("Redo");\r
659     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
660     {\r
661       public void actionPerformed(ActionEvent e)\r
662       {\r
663         redoMenuItem_actionPerformed(e);\r
664       }\r
665     });\r
666     conservationMenuItem.setText("By Conservation");\r
667     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
668     {\r
669       public void actionPerformed(ActionEvent e)\r
670       {\r
671         conservationMenuItem_actionPerformed(e);\r
672       }\r
673     });\r
674     noColourmenuItem.setText("None");\r
675     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
676     {\r
677       public void actionPerformed(ActionEvent e)\r
678       {\r
679         noColourmenuItem_actionPerformed(e);\r
680       }\r
681     });\r
682     wrapMenuItem.setText("Wrap");\r
683     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
684     {\r
685       public void actionPerformed(ActionEvent e)\r
686       {\r
687         wrapMenuItem_actionPerformed(e);\r
688       }\r
689     });\r
690     printMenuItem.setText("Print");\r
691     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
692     {\r
693       public void actionPerformed(ActionEvent e)\r
694       {\r
695         printMenuItem_actionPerformed(e);\r
696       }\r
697     });\r
698     renderGapsMenuItem.setText("Show Gaps");\r
699     renderGapsMenuItem.setState(true);\r
700     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
701     {\r
702       public void actionPerformed(ActionEvent e)\r
703       {\r
704         renderGapsMenuItem_actionPerformed(e);\r
705       }\r
706     });\r
707     findMenuItem.setText("Find...");\r
708     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
709         java.awt.event.KeyEvent.VK_F,\r
710         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
711     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
712     {\r
713       public void actionPerformed(ActionEvent e)\r
714       {\r
715         findMenuItem_actionPerformed(e);\r
716       }\r
717     });\r
718     searchMenu.setText("Search");\r
719 \r
720     abovePIDThreshold.setText("Above Identity Threshold");\r
721     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
722     {\r
723       public void actionPerformed(ActionEvent e)\r
724       {\r
725         abovePIDThreshold_actionPerformed(e);\r
726       }\r
727     });\r
728     showSeqFeatures.setText("Show Sequence Features");\r
729     showSeqFeatures.addActionListener(new ActionListener()\r
730     {\r
731       public void actionPerformed(ActionEvent actionEvent)\r
732       {\r
733         showSeqFeatures_actionPerformed(actionEvent);\r
734       }\r
735     });\r
736     nucleotideColour.setText("Nucleotide");\r
737     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
738     {\r
739       public void actionPerformed(ActionEvent e)\r
740       {\r
741         nucleotideColour_actionPerformed(e);\r
742       }\r
743     });\r
744     deleteGroups.setText("Undefine groups");\r
745     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
746     {\r
747       public void actionPerformed(ActionEvent e)\r
748       {\r
749         deleteGroups_actionPerformed(e);\r
750       }\r
751     });\r
752     copy.setText("Copy");\r
753     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
754         java.awt.event.KeyEvent.VK_C,\r
755         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
756     copy.setMnemonic(KeyEvent.VK_C);\r
757 \r
758     copy.addActionListener(new java.awt.event.ActionListener()\r
759     {\r
760       public void actionPerformed(ActionEvent e)\r
761       {\r
762         copy_actionPerformed(e);\r
763       }\r
764     });\r
765     cut.setText("Cut");\r
766     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
767         java.awt.event.KeyEvent.VK_X,\r
768         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
769     cut.setMnemonic(KeyEvent.VK_X);\r
770     cut.addActionListener(new java.awt.event.ActionListener()\r
771     {\r
772       public void actionPerformed(ActionEvent e)\r
773       {\r
774         cut_actionPerformed(e);\r
775       }\r
776     });\r
777     delete.setText("Delete");\r
778     delete.addActionListener(new java.awt.event.ActionListener()\r
779     {\r
780       public void actionPerformed(ActionEvent e)\r
781       {\r
782         delete_actionPerformed(e);\r
783       }\r
784     });\r
785     jMenu1.setMnemonic('V');\r
786     jMenu1.setText("Paste");\r
787     pasteNew.setText("To New Alignment");\r
788     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
789         java.awt.event.KeyEvent.VK_V,\r
790         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
791     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
792     {\r
793       public void actionPerformed(ActionEvent e)\r
794       {\r
795         pasteNew_actionPerformed(e);\r
796       }\r
797     });\r
798     pasteThis.setText("Add To This Alignment");\r
799     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
800     {\r
801       public void actionPerformed(ActionEvent e)\r
802       {\r
803         pasteThis_actionPerformed(e);\r
804       }\r
805     });\r
806     applyToAllGroups.setText("Apply Colour To All Groups");\r
807     applyToAllGroups.setState(true);\r
808     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
809     {\r
810       public void actionPerformed(ActionEvent e)\r
811       {\r
812         applyToAllGroups_actionPerformed(e);\r
813       }\r
814     });\r
815     createPNG.addActionListener(new java.awt.event.ActionListener()\r
816     {\r
817       public void actionPerformed(ActionEvent e)\r
818       {\r
819         createPNG(null);\r
820       }\r
821     });\r
822     createPNG.setActionCommand("Save As PNG Image");\r
823     createPNG.setText("PNG");\r
824     font.setText("Font...");\r
825     font.addActionListener(new java.awt.event.ActionListener()\r
826     {\r
827       public void actionPerformed(ActionEvent e)\r
828       {\r
829         font_actionPerformed(e);\r
830       }\r
831     });\r
832 \r
833     seqLimits.setText("Show Sequence Limits");\r
834     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
835     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
836     {\r
837       public void actionPerformed(ActionEvent e)\r
838       {\r
839         seqLimit_actionPerformed(e);\r
840       }\r
841     });\r
842     epsFile.setText("EPS");\r
843     epsFile.addActionListener(new java.awt.event.ActionListener()\r
844     {\r
845       public void actionPerformed(ActionEvent e)\r
846       {\r
847         createEPS(null);\r
848       }\r
849     });\r
850     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
851     LoadtreeMenuItem.setText("Load Associated Tree");\r
852     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
853     {\r
854       public void actionPerformed(ActionEvent e)\r
855       {\r
856         LoadtreeMenuItem_actionPerformed(e);\r
857       }\r
858     });\r
859     scaleAbove.setVisible(false);\r
860     scaleAbove.setText("Scale Above");\r
861     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
862     {\r
863       public void actionPerformed(ActionEvent e)\r
864       {\r
865         scaleAbove_actionPerformed(e);\r
866       }\r
867     });\r
868     scaleLeft.setVisible(false);\r
869     scaleLeft.setSelected(true);\r
870     scaleLeft.setText("Scale Left");\r
871     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
872     {\r
873       public void actionPerformed(ActionEvent e)\r
874       {\r
875         scaleLeft_actionPerformed(e);\r
876       }\r
877     });\r
878     scaleRight.setVisible(false);\r
879     scaleRight.setSelected(true);\r
880     scaleRight.setText("Scale Right");\r
881     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
882     {\r
883       public void actionPerformed(ActionEvent e)\r
884       {\r
885         scaleRight_actionPerformed(e);\r
886       }\r
887     });\r
888     modifyPID.setText("Modify Identity Threshold...");\r
889     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
890     {\r
891       public void actionPerformed(ActionEvent e)\r
892       {\r
893         modifyPID_actionPerformed(e);\r
894       }\r
895     });\r
896     modifyConservation.setText("Modify Conservation Threshold...");\r
897     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
898     {\r
899       public void actionPerformed(ActionEvent e)\r
900       {\r
901         modifyConservation_actionPerformed(e);\r
902       }\r
903     });\r
904     sortByTreeMenu.setText("By Tree Order");\r
905     sort.setText("Sort");\r
906     calculate.setText("Calculate Tree");\r
907 \r
908     jMenu2.setText("Export");\r
909     padGapsMenuitem.setText("Pad Gaps");\r
910     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
911     padGapsMenuitem.addActionListener(new ActionListener()\r
912     {\r
913       public void actionPerformed(ActionEvent e)\r
914       {\r
915         padGapsMenuitem_actionPerformed(e);\r
916       }\r
917     });\r
918     vamsasStore.setVisible(false);\r
919     vamsasStore.setText("VAMSAS store");\r
920     vamsasStore.addActionListener(new ActionListener()\r
921     {\r
922       public void actionPerformed(ActionEvent e)\r
923       {\r
924         vamsasStore_actionPerformed(e);\r
925       }\r
926     });\r
927     showTranslation.setText("Translate cDNA");\r
928     showTranslation.addActionListener(new ActionListener()\r
929     {\r
930       public void actionPerformed(ActionEvent e)\r
931       {\r
932         showTranslation_actionPerformed(e);\r
933       }\r
934     });\r
935 \r
936    /* tabbedPane.addChangeListener(new ChangeListener()\r
937         {\r
938           public void stateChanged(ChangeEvent ece)\r
939           {\r
940 \r
941             tabSelected();\r
942           }\r
943         });*/\r
944     featureSettings.setText("Feature Settings...");\r
945     featureSettings.addActionListener(new ActionListener()\r
946     {\r
947       public void actionPerformed(ActionEvent e)\r
948       {\r
949         featureSettings_actionPerformed(e);\r
950       }\r
951     });\r
952     fetchSequence.setText("Fetch Sequence(s)...");\r
953     fetchSequence.addActionListener(new ActionListener()\r
954     {\r
955       public void actionPerformed(ActionEvent e)\r
956       {\r
957         fetchSequence_actionPerformed(e);\r
958       }\r
959     });\r
960     smoothFont.setText("Smooth Fonts");\r
961     smoothFont.addActionListener(new ActionListener()\r
962     {\r
963       public void actionPerformed(ActionEvent e)\r
964       {\r
965         smoothFont_actionPerformed(e);\r
966       }\r
967     });\r
968     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
969     annotationColour.setText("By Annotation...");\r
970     annotationColour.addActionListener(new ActionListener()\r
971     {\r
972       public void actionPerformed(ActionEvent e)\r
973       {\r
974         annotationColour_actionPerformed(e);\r
975       }\r
976     });\r
977     associatedData.setText("Load Features / Annotations");\r
978     associatedData.addActionListener(new ActionListener()\r
979     {\r
980       public void actionPerformed(ActionEvent e)\r
981       {\r
982         associatedData_actionPerformed(e);\r
983       }\r
984     });\r
985     autoCalculate.setText("Autocalculate Consensus");\r
986     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
987     autoCalculate.addActionListener(new ActionListener()\r
988     {\r
989       public void actionPerformed(ActionEvent e)\r
990       {\r
991         autoCalculate_actionPerformed(e);\r
992       }\r
993     });\r
994     addSequenceMenu.setText("Add Sequences");\r
995     addFromFile.setText("From File");\r
996     addFromFile.addActionListener(new ActionListener()\r
997     {\r
998       public void actionPerformed(ActionEvent e)\r
999       {\r
1000         addFromFile_actionPerformed(e);\r
1001       }\r
1002     });\r
1003     addFromText.setText("From Textbox");\r
1004     addFromText.addActionListener(new ActionListener()\r
1005     {\r
1006       public void actionPerformed(ActionEvent e)\r
1007       {\r
1008         addFromText_actionPerformed(e);\r
1009       }\r
1010     });\r
1011     addFromURL.setText("From URL");\r
1012     addFromURL.addActionListener(new ActionListener()\r
1013     {\r
1014       public void actionPerformed(ActionEvent e)\r
1015       {\r
1016         addFromURL_actionPerformed(e);\r
1017       }\r
1018     });\r
1019     exportFeatures.setText("Export Features...");\r
1020     exportFeatures.addActionListener(new ActionListener()\r
1021     {\r
1022       public void actionPerformed(ActionEvent e)\r
1023       {\r
1024         exportFeatures_actionPerformed(e);\r
1025       }\r
1026     });\r
1027     exportAnnotations.setText("Export Annotations...");\r
1028     exportAnnotations.addActionListener(new ActionListener()\r
1029     {\r
1030       public void actionPerformed(ActionEvent e)\r
1031       {\r
1032         exportAnnotations_actionPerformed(e);\r
1033       }\r
1034     });\r
1035     statusPanel.setLayout(gridLayout1);\r
1036     jMenu3.setText("Show");\r
1037     showAllSeqs.setText("All Sequences");\r
1038     showAllSeqs.addActionListener(new ActionListener()\r
1039     {\r
1040       public void actionPerformed(ActionEvent e)\r
1041       {\r
1042         showAllSeqs_actionPerformed(e);\r
1043       }\r
1044     });\r
1045     showAllColumns.setText("All Columns");\r
1046     showAllColumns.addActionListener(new ActionListener()\r
1047     {\r
1048       public void actionPerformed(ActionEvent e)\r
1049       {\r
1050         showAllColumns_actionPerformed(e);\r
1051       }\r
1052     });\r
1053     jMenu4.setText("Hide");\r
1054     hideSelSequences.setText("Selected Sequences");\r
1055     hideSelSequences.addActionListener(new ActionListener()\r
1056     {\r
1057       public void actionPerformed(ActionEvent e)\r
1058       {\r
1059         hideSelSequences_actionPerformed(e);\r
1060       }\r
1061     });\r
1062     hideSelColumns.setText("Selected Columns");\r
1063     hideSelColumns.addActionListener(new ActionListener()\r
1064     {\r
1065       public void actionPerformed(ActionEvent e)\r
1066       {\r
1067         hideSelColumns_actionPerformed(e);\r
1068       }\r
1069     });\r
1070     hiddenMarkers.setText("Hidden Markers");\r
1071     hiddenMarkers.setState(true);\r
1072     hiddenMarkers.addActionListener(new ActionListener()\r
1073     {\r
1074       public void actionPerformed(ActionEvent e)\r
1075       {\r
1076         hiddenMarkers_actionPerformed(e);\r
1077       }\r
1078     });\r
1079     alignFrameMenuBar.add(fileMenu);\r
1080     alignFrameMenuBar.add(editMenu);\r
1081     alignFrameMenuBar.add(searchMenu);\r
1082     alignFrameMenuBar.add(viewMenu);\r
1083     alignFrameMenuBar.add(colourMenu);\r
1084     alignFrameMenuBar.add(calculateMenu);\r
1085     alignFrameMenuBar.add(webService);\r
1086     fileMenu.add(addSequenceMenu);\r
1087     fileMenu.add(fetchSequence);\r
1088     fileMenu.addSeparator();\r
1089     fileMenu.add(vamsasStore);\r
1090     fileMenu.add(saveAlignmentMenu);\r
1091     fileMenu.add(jMenu2);\r
1092     fileMenu.add(outputTextboxMenu);\r
1093     fileMenu.add(printMenuItem);\r
1094     fileMenu.addSeparator();\r
1095     fileMenu.add(exportFeatures);\r
1096     fileMenu.add(exportAnnotations);\r
1097     fileMenu.add(LoadtreeMenuItem);\r
1098     fileMenu.add(associatedData);\r
1099     fileMenu.addSeparator();\r
1100     fileMenu.add(closeMenuItem);\r
1101     editMenu.add(undoMenuItem);\r
1102     editMenu.add(redoMenuItem);\r
1103     editMenu.add(cut);\r
1104     editMenu.add(copy);\r
1105     editMenu.add(jMenu1);\r
1106     editMenu.add(delete);\r
1107     editMenu.addSeparator();\r
1108     editMenu.add(selectAllSequenceMenuItem);\r
1109     editMenu.add(deselectAllSequenceMenuItem);\r
1110     editMenu.add(invertSequenceMenuItem);\r
1111     editMenu.add(deleteGroups);\r
1112     editMenu.addSeparator();\r
1113     editMenu.add(remove2LeftMenuItem);\r
1114     editMenu.add(remove2RightMenuItem);\r
1115     editMenu.add(removeGappedColumnMenuItem);\r
1116     editMenu.add(removeAllGapsMenuItem);\r
1117     editMenu.add(removeRedundancyMenuItem);\r
1118     editMenu.addSeparator();\r
1119     editMenu.add(padGapsMenuitem);\r
1120     searchMenu.add(findMenuItem);\r
1121     viewMenu.add(font);\r
1122     viewMenu.add(smoothFont);\r
1123     viewMenu.addSeparator();\r
1124     viewMenu.add(jMenu3);\r
1125     viewMenu.add(jMenu4);\r
1126     viewMenu.add(hiddenMarkers);\r
1127     viewMenu.addSeparator();\r
1128     viewMenu.add(wrapMenuItem);\r
1129     viewMenu.add(seqLimits);\r
1130     viewMenu.add(scaleAbove);\r
1131     viewMenu.add(scaleLeft);\r
1132     viewMenu.add(scaleRight);\r
1133     viewMenu.add(viewBoxesMenuItem);\r
1134     viewMenu.add(viewTextMenuItem);\r
1135     viewMenu.add(colourTextMenuItem);\r
1136     viewMenu.add(renderGapsMenuItem);\r
1137     viewMenu.add(annotationPanelMenuItem);\r
1138     viewMenu.addSeparator();\r
1139     viewMenu.add(showSeqFeatures);\r
1140     viewMenu.add(featureSettings);\r
1141     viewMenu.addSeparator();\r
1142     viewMenu.add(overviewMenuItem);\r
1143     colourMenu.add(applyToAllGroups);\r
1144     colourMenu.addSeparator();\r
1145     colourMenu.add(noColourmenuItem);\r
1146     colourMenu.add(clustalColour);\r
1147     colourMenu.add(BLOSUM62Colour);\r
1148     colourMenu.add(PIDColour);\r
1149     colourMenu.add(zappoColour);\r
1150     colourMenu.add(taylorColour);\r
1151     colourMenu.add(hydrophobicityColour);\r
1152     colourMenu.add(helixColour);\r
1153     colourMenu.add(strandColour);\r
1154     colourMenu.add(turnColour);\r
1155     colourMenu.add(buriedColour);\r
1156     colourMenu.add(nucleotideColour);\r
1157     colourMenu.add(userDefinedColour);\r
1158     colourMenu.addSeparator();\r
1159     colourMenu.add(conservationMenuItem);\r
1160     colourMenu.add(modifyConservation);\r
1161     colourMenu.add(abovePIDThreshold);\r
1162     colourMenu.add(modifyPID);\r
1163     colourMenu.add(annotationColour);\r
1164     calculateMenu.add(sort);\r
1165     calculateMenu.add(calculate);\r
1166     calculateMenu.addSeparator();\r
1167     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1168     calculateMenu.add(PCAMenuItem);\r
1169     calculateMenu.addSeparator();\r
1170     calculateMenu.add(showTranslation);\r
1171     calculateMenu.add(autoCalculate);\r
1172     webServiceNoServices=new JMenuItem("<No Services>");\r
1173     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1174     jMenu1.add(pasteThis);\r
1175     sort.add(sortIDMenuItem);\r
1176     sort.add(sortGroupMenuItem);\r
1177     sort.add(sortPairwiseMenuItem);\r
1178     calculate.add(averageDistanceTreeMenuItem);\r
1179     calculate.add(neighbourTreeMenuItem);\r
1180     calculate.add(avDistanceTreeBlosumMenuItem);\r
1181     calculate.add(njTreeBlosumMenuItem);\r
1182     jMenu2.add(htmlMenuItem);\r
1183     jMenu2.add(epsFile);\r
1184     jMenu2.add(createPNG);\r
1185     addSequenceMenu.add(addFromFile);\r
1186     addSequenceMenu.add(addFromText);\r
1187     addSequenceMenu.add(addFromURL);\r
1188     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1189     statusPanel.add(statusBar, null);\r
1190     jMenu3.add(showAllColumns);\r
1191     jMenu3.add(showAllSeqs);\r
1192     jMenu4.add(hideSelColumns);\r
1193     jMenu4.add(hideSelSequences);\r
1194   }\r
1195 \r
1196   protected void outputText_actionPerformed(ActionEvent e)\r
1197   {\r
1198   }\r
1199 \r
1200   public void addFromFile_actionPerformed(ActionEvent e)\r
1201   {\r
1202 \r
1203   }\r
1204 \r
1205   public void addFromText_actionPerformed(ActionEvent e)\r
1206   {\r
1207 \r
1208   }\r
1209 \r
1210   public void addFromURL_actionPerformed(ActionEvent e)\r
1211   {\r
1212 \r
1213   }\r
1214 \r
1215   public void exportFeatures_actionPerformed(ActionEvent e)\r
1216   {\r
1217 \r
1218   }\r
1219 \r
1220   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1221   {\r
1222 \r
1223   }\r
1224 \r
1225   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1226   {\r
1227   }\r
1228 \r
1229   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1230   {\r
1231   }\r
1232 \r
1233   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1234   {\r
1235   }\r
1236 \r
1237   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1238   {\r
1239   }\r
1240 \r
1241   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1242   {\r
1243   }\r
1244 \r
1245   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1246   {\r
1247   }\r
1248 \r
1249   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1250   {\r
1251   }\r
1252 \r
1253   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1254   {\r
1255   }\r
1256 \r
1257   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1258   {\r
1259   }\r
1260 \r
1261   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1262   {\r
1263   }\r
1264 \r
1265   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1266   {\r
1267   }\r
1268 \r
1269   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1270   {\r
1271   }\r
1272 \r
1273   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1274   {\r
1275   }\r
1276 \r
1277   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1278   {\r
1279   }\r
1280 \r
1281   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1282   {\r
1283   }\r
1284 \r
1285   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1286   {\r
1287   }\r
1288 \r
1289   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1290   {\r
1291   }\r
1292 \r
1293   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1294   {\r
1295   }\r
1296 \r
1297   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1298   {\r
1299   }\r
1300 \r
1301   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1302   {\r
1303   }\r
1304 \r
1305   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1306   {\r
1307   }\r
1308 \r
1309   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1310   {\r
1311   }\r
1312 \r
1313   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1314   {\r
1315   }\r
1316 \r
1317   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1318   {\r
1319   }\r
1320 \r
1321   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1322   {\r
1323   }\r
1324 \r
1325   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1326   {\r
1327   }\r
1328 \r
1329   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1330   {\r
1331   }\r
1332 \r
1333   protected void clustalColour_actionPerformed(ActionEvent e)\r
1334   {\r
1335   }\r
1336 \r
1337   protected void zappoColour_actionPerformed(ActionEvent e)\r
1338   {\r
1339   }\r
1340 \r
1341   protected void taylorColour_actionPerformed(ActionEvent e)\r
1342   {\r
1343   }\r
1344 \r
1345   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1346   {\r
1347   }\r
1348 \r
1349   protected void helixColour_actionPerformed(ActionEvent e)\r
1350   {\r
1351   }\r
1352 \r
1353   protected void strandColour_actionPerformed(ActionEvent e)\r
1354   {\r
1355   }\r
1356 \r
1357   protected void turnColour_actionPerformed(ActionEvent e)\r
1358   {\r
1359   }\r
1360 \r
1361   protected void buriedColour_actionPerformed(ActionEvent e)\r
1362   {\r
1363   }\r
1364 \r
1365   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1366   {\r
1367   }\r
1368 \r
1369   protected void PIDColour_actionPerformed(ActionEvent e)\r
1370   {\r
1371   }\r
1372 \r
1373   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1374   {\r
1375   }\r
1376 \r
1377   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1378   {\r
1379   }\r
1380 \r
1381   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1382   {\r
1383   }\r
1384 \r
1385   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1386   {\r
1387   }\r
1388 \r
1389   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1390   {\r
1391   }\r
1392 \r
1393   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1394   {\r
1395   }\r
1396 \r
1397   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1398   {\r
1399   }\r
1400 \r
1401   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1402   {\r
1403   }\r
1404 \r
1405   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1406   {\r
1407   }\r
1408 \r
1409   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1410   {\r
1411   }\r
1412 \r
1413   protected void copy_actionPerformed(ActionEvent e)\r
1414   {\r
1415   }\r
1416 \r
1417   protected void cut_actionPerformed(ActionEvent e)\r
1418   {\r
1419   }\r
1420 \r
1421   protected void delete_actionPerformed(ActionEvent e)\r
1422   {\r
1423   }\r
1424 \r
1425   protected void pasteNew_actionPerformed(ActionEvent e)\r
1426   {\r
1427   }\r
1428 \r
1429   protected void pasteThis_actionPerformed(ActionEvent e)\r
1430   {\r
1431   }\r
1432 \r
1433   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1434   {\r
1435   }\r
1436 \r
1437   public void createPNG(java.io.File f)\r
1438   {\r
1439   }\r
1440 \r
1441   protected void font_actionPerformed(ActionEvent e)\r
1442   {\r
1443   }\r
1444 \r
1445   protected void seqLimit_actionPerformed(ActionEvent e)\r
1446   {\r
1447   }\r
1448 \r
1449   public void seqDBRef_actionPerformed(ActionEvent e)\r
1450   {\r
1451 \r
1452   }\r
1453 \r
1454 \r
1455   public void createEPS(java.io.File f)\r
1456   {\r
1457   }\r
1458 \r
1459   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1460   {\r
1461   }\r
1462 \r
1463   protected void jpred_actionPerformed(ActionEvent e)\r
1464   {\r
1465   }\r
1466 \r
1467   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1468   {\r
1469   }\r
1470 \r
1471   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1472   {\r
1473   }\r
1474 \r
1475   protected void scaleRight_actionPerformed(ActionEvent e)\r
1476   {\r
1477   }\r
1478 \r
1479   protected void modifyPID_actionPerformed(ActionEvent e)\r
1480   {\r
1481   }\r
1482 \r
1483   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1484   {\r
1485   }\r
1486 \r
1487 \r
1488 \r
1489   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1490   {\r
1491   }\r
1492 \r
1493   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1494   {\r
1495   }\r
1496 \r
1497 \r
1498   public void vamsasStore_actionPerformed(ActionEvent e)\r
1499   {\r
1500 \r
1501   }\r
1502 \r
1503   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1504   {\r
1505 \r
1506   }\r
1507 \r
1508   public void showTranslation_actionPerformed(ActionEvent e)\r
1509   {\r
1510 \r
1511   }\r
1512 \r
1513   public void featureSettings_actionPerformed(ActionEvent e)\r
1514   {\r
1515 \r
1516   }\r
1517 \r
1518   public void fetchSequence_actionPerformed(ActionEvent e)\r
1519   {\r
1520 \r
1521   }\r
1522 \r
1523   public void smoothFont_actionPerformed(ActionEvent e)\r
1524   {\r
1525 \r
1526   }\r
1527 \r
1528   public void annotationColour_actionPerformed(ActionEvent e)\r
1529   {\r
1530 \r
1531   }\r
1532 \r
1533 \r
1534   public void associatedData_actionPerformed(ActionEvent e)\r
1535   {\r
1536 \r
1537   }\r
1538 \r
1539   public void autoCalculate_actionPerformed(ActionEvent e)\r
1540   {\r
1541 \r
1542   }\r
1543 \r
1544   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1545   {\r
1546 \r
1547   }\r
1548 \r
1549   public void showAllColumns_actionPerformed(ActionEvent e)\r
1550   {\r
1551 \r
1552   }\r
1553 \r
1554   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1555   {\r
1556 \r
1557   }\r
1558 \r
1559   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1560   {\r
1561 \r
1562   }\r
1563 \r
1564   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1565   {\r
1566 \r
1567   }\r
1568 }\r