elementAt instead of get for 1.1 compatibility
[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   JMenuItem invertColSel = new JMenuItem();\r
140 \r
141   public GAlignFrame()\r
142   {\r
143 \r
144 \r
145     try\r
146     {\r
147       jbInit();\r
148       setJMenuBar(alignFrameMenuBar);\r
149 \r
150       // dynamically fill save as menu with available formats\r
151       for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
152       {\r
153         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
154                              elementAt(\r
155                                  i));\r
156         item.addActionListener(new java.awt.event.ActionListener()\r
157         {\r
158           public void actionPerformed(ActionEvent e)\r
159           {\r
160             outputText_actionPerformed(e);\r
161           }\r
162         });\r
163 \r
164         outputTextboxMenu.add(item);\r
165       }\r
166     }\r
167     catch (Exception e)\r
168     {\r
169     }\r
170 \r
171 \r
172     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
173     {\r
174       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
175           getUserColourSchemes().keys();\r
176 \r
177       while (userColours.hasMoreElements())\r
178       {\r
179         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
180             nextElement().toString());\r
181         radioItem.setName("USER_DEFINED");\r
182         radioItem.addMouseListener(new MouseAdapter()\r
183             {\r
184               public void mousePressed(MouseEvent evt)\r
185               {\r
186                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
187                 {\r
188                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
189 \r
190                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
191                       "Remove from default list?",\r
192                       "Remove user defined colour",\r
193                       JOptionPane.YES_NO_OPTION);\r
194                   if(option == JOptionPane.YES_OPTION)\r
195                   {\r
196                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
197                     colourMenu.remove(radioItem);\r
198                   }\r
199                   else\r
200                     radioItem.addActionListener(new ActionListener()\r
201                     {\r
202                       public void actionPerformed(ActionEvent evt)\r
203                       {\r
204                         userDefinedColour_actionPerformed(evt);\r
205                       }\r
206                     });\r
207                 }\r
208               }\r
209             });\r
210         radioItem.addActionListener(new ActionListener()\r
211         {\r
212           public void actionPerformed(ActionEvent evt)\r
213           {\r
214             userDefinedColour_actionPerformed(evt);\r
215           }\r
216         });\r
217         colourMenu.insert(radioItem, 15);\r
218         colours.add(radioItem);\r
219       }\r
220     }\r
221     colours.add(noColourmenuItem);\r
222     colours.add(clustalColour);\r
223     colours.add(zappoColour);\r
224     colours.add(taylorColour);\r
225     colours.add(hydrophobicityColour);\r
226     colours.add(helixColour);\r
227     colours.add(strandColour);\r
228     colours.add(turnColour);\r
229     colours.add(buriedColour);\r
230     colours.add(userDefinedColour);\r
231     colours.add(PIDColour);\r
232     colours.add(BLOSUM62Colour);\r
233     colours.add(nucleotideColour);\r
234 \r
235     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
236 \r
237 \r
238   }\r
239 \r
240   public void setColourSelected(String defaultColour)\r
241   {\r
242 \r
243     if (defaultColour != null)\r
244     {\r
245       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
246 \r
247       switch (index)\r
248       {\r
249         case ColourSchemeProperty.NONE:\r
250               noColourmenuItem.setSelected(true);\r
251               break;\r
252         case ColourSchemeProperty.CLUSTAL:\r
253           clustalColour.setSelected(true);\r
254 \r
255           break;\r
256 \r
257         case ColourSchemeProperty.BLOSUM:\r
258           BLOSUM62Colour.setSelected(true);\r
259 \r
260           break;\r
261 \r
262         case ColourSchemeProperty.PID:\r
263           PIDColour.setSelected(true);\r
264 \r
265           break;\r
266 \r
267         case ColourSchemeProperty.ZAPPO:\r
268           zappoColour.setSelected(true);\r
269 \r
270           break;\r
271 \r
272         case ColourSchemeProperty.TAYLOR:\r
273           taylorColour.setSelected(true);\r
274           break;\r
275 \r
276         case ColourSchemeProperty.HYDROPHOBIC:\r
277           hydrophobicityColour.setSelected(true);\r
278 \r
279           break;\r
280 \r
281         case ColourSchemeProperty.HELIX:\r
282           helixColour.setSelected(true);\r
283 \r
284           break;\r
285 \r
286         case ColourSchemeProperty.STRAND:\r
287           strandColour.setSelected(true);\r
288 \r
289           break;\r
290 \r
291         case ColourSchemeProperty.TURN:\r
292           turnColour.setSelected(true);\r
293 \r
294           break;\r
295 \r
296         case ColourSchemeProperty.BURIED:\r
297           buriedColour.setSelected(true);\r
298 \r
299           break;\r
300 \r
301         case ColourSchemeProperty.NUCLEOTIDE:\r
302           nucleotideColour.setSelected(true);\r
303 \r
304           break;\r
305 \r
306         case ColourSchemeProperty.USER_DEFINED:\r
307           userDefinedColour.setSelected(true);\r
308 \r
309           break;\r
310       }\r
311     }\r
312 \r
313   }\r
314 \r
315   private void jbInit()\r
316       throws Exception\r
317   {\r
318     fileMenu.setMnemonic('F');\r
319     fileMenu.setText("File");\r
320     saveAlignmentMenu.setMnemonic('L');\r
321     saveAlignmentMenu.setText("Save As");\r
322     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
323         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
324     saveAlignmentMenu.addActionListener(new ActionListener()\r
325     {\r
326       public void actionPerformed(ActionEvent e)\r
327       {\r
328         saveAlignmentMenu_actionPerformed(e);\r
329       }\r
330     });\r
331     closeMenuItem.setMnemonic('C');\r
332     closeMenuItem.setText("Close");\r
333     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
334     {\r
335       public void actionPerformed(ActionEvent e)\r
336       {\r
337         closeMenuItem_actionPerformed(e);\r
338       }\r
339     });\r
340     editMenu.setText("Edit");\r
341     viewMenu.setText("View");\r
342     colourMenu.setText("Colour");\r
343     calculateMenu.setText("Calculate");\r
344     webService.setText("Web Service");\r
345     selectAllSequenceMenuItem.setText("Select all");\r
346     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
347         java.awt.event.KeyEvent.VK_A,\r
348         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
349     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
350                                                 ActionListener()\r
351     {\r
352       public void actionPerformed(ActionEvent e)\r
353       {\r
354         selectAllSequenceMenuItem_actionPerformed(e);\r
355       }\r
356     });\r
357     deselectAllSequenceMenuItem.setText("Deselect All");\r
358     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
359                                                getKeyStroke(\r
360         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
361     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
362                                                   ActionListener()\r
363     {\r
364       public void actionPerformed(ActionEvent e)\r
365       {\r
366         deselectAllSequenceMenuItem_actionPerformed(e);\r
367       }\r
368     });\r
369     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
370     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
371     {\r
372       public void actionPerformed(ActionEvent e)\r
373       {\r
374         invertSequenceMenuItem_actionPerformed(e);\r
375       }\r
376     });\r
377     remove2LeftMenuItem.setText("Remove Left");\r
378     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
379     {\r
380       public void actionPerformed(ActionEvent e)\r
381       {\r
382         remove2LeftMenuItem_actionPerformed(e);\r
383       }\r
384     });\r
385     remove2RightMenuItem.setText("Remove Right");\r
386     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
387     {\r
388       public void actionPerformed(ActionEvent e)\r
389       {\r
390         remove2RightMenuItem_actionPerformed(e);\r
391       }\r
392     });\r
393     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
394     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
395                                                  ActionListener()\r
396     {\r
397       public void actionPerformed(ActionEvent e)\r
398       {\r
399         removeGappedColumnMenuItem_actionPerformed(e);\r
400       }\r
401     });\r
402     removeAllGapsMenuItem.setText("Remove All Gaps");\r
403     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
404     {\r
405       public void actionPerformed(ActionEvent e)\r
406       {\r
407         removeAllGapsMenuItem_actionPerformed(e);\r
408       }\r
409     });\r
410     viewBoxesMenuItem.setText("Boxes");\r
411     viewBoxesMenuItem.setState(true);\r
412     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
413     {\r
414       public void actionPerformed(ActionEvent e)\r
415       {\r
416         viewBoxesMenuItem_actionPerformed(e);\r
417       }\r
418     });\r
419     viewTextMenuItem.setText("Text");\r
420     viewTextMenuItem.setState(true);\r
421     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
422     {\r
423       public void actionPerformed(ActionEvent e)\r
424       {\r
425         viewTextMenuItem_actionPerformed(e);\r
426       }\r
427     });\r
428     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
429     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
430     {\r
431       public void actionPerformed(ActionEvent e)\r
432       {\r
433         sortPairwiseMenuItem_actionPerformed(e);\r
434       }\r
435     });\r
436     sortIDMenuItem.setText("by ID");\r
437     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
438     {\r
439       public void actionPerformed(ActionEvent e)\r
440       {\r
441         sortIDMenuItem_actionPerformed(e);\r
442       }\r
443     });\r
444     sortGroupMenuItem.setText("by Group");\r
445     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
446     {\r
447       public void actionPerformed(ActionEvent e)\r
448       {\r
449         sortGroupMenuItem_actionPerformed(e);\r
450       }\r
451     });\r
452     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
453     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
454                                                ActionListener()\r
455     {\r
456       public void actionPerformed(ActionEvent e)\r
457       {\r
458         removeRedundancyMenuItem_actionPerformed(e);\r
459       }\r
460     });\r
461     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
462     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
463                                                 ActionListener()\r
464     {\r
465       public void actionPerformed(ActionEvent e)\r
466       {\r
467         pairwiseAlignmentMenuItem_actionPerformed(e);\r
468       }\r
469     });\r
470     PCAMenuItem.setText("Principal Component Analysis");\r
471     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
472     {\r
473       public void actionPerformed(ActionEvent e)\r
474       {\r
475         PCAMenuItem_actionPerformed(e);\r
476       }\r
477     });\r
478     averageDistanceTreeMenuItem.setText(\r
479         "Average Distance Using % Identity");\r
480     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
481                                                   ActionListener()\r
482     {\r
483       public void actionPerformed(ActionEvent e)\r
484       {\r
485         averageDistanceTreeMenuItem_actionPerformed(e);\r
486       }\r
487     });\r
488     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
489     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
490     {\r
491       public void actionPerformed(ActionEvent e)\r
492       {\r
493         neighbourTreeMenuItem_actionPerformed(e);\r
494       }\r
495     });\r
496     this.getContentPane().setLayout(borderLayout1);\r
497     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
498     statusBar.setBackground(Color.white);\r
499     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
500     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
501     statusBar.setText("Status bar");\r
502     outputTextboxMenu.setMnemonic('T');\r
503     outputTextboxMenu.setText("Output to Textbox");\r
504     clustalColour.setText("Clustalx");\r
505 \r
506     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
507     {\r
508       public void actionPerformed(ActionEvent e)\r
509       {\r
510         clustalColour_actionPerformed(e);\r
511       }\r
512     });\r
513     zappoColour.setText("Zappo");\r
514     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
515     {\r
516       public void actionPerformed(ActionEvent e)\r
517       {\r
518         zappoColour_actionPerformed(e);\r
519       }\r
520     });\r
521     taylorColour.setText("Taylor");\r
522     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
523     {\r
524       public void actionPerformed(ActionEvent e)\r
525       {\r
526         taylorColour_actionPerformed(e);\r
527       }\r
528     });\r
529     hydrophobicityColour.setText("Hydrophobicity");\r
530     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
531     {\r
532       public void actionPerformed(ActionEvent e)\r
533       {\r
534         hydrophobicityColour_actionPerformed(e);\r
535       }\r
536     });\r
537     helixColour.setText("Helix Propensity");\r
538     helixColour.addActionListener(new java.awt.event.ActionListener()\r
539     {\r
540       public void actionPerformed(ActionEvent e)\r
541       {\r
542         helixColour_actionPerformed(e);\r
543       }\r
544     });\r
545     strandColour.setText("Strand Propensity");\r
546     strandColour.addActionListener(new java.awt.event.ActionListener()\r
547     {\r
548       public void actionPerformed(ActionEvent e)\r
549       {\r
550         strandColour_actionPerformed(e);\r
551       }\r
552     });\r
553     turnColour.setText("Turn Propensity");\r
554     turnColour.addActionListener(new java.awt.event.ActionListener()\r
555     {\r
556       public void actionPerformed(ActionEvent e)\r
557       {\r
558         turnColour_actionPerformed(e);\r
559       }\r
560     });\r
561     buriedColour.setText("Buried Index");\r
562     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
563     {\r
564       public void actionPerformed(ActionEvent e)\r
565       {\r
566         buriedColour_actionPerformed(e);\r
567       }\r
568     });\r
569     userDefinedColour.setText("User Defined...");\r
570     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
571     {\r
572       public void actionPerformed(ActionEvent e)\r
573       {\r
574         userDefinedColour_actionPerformed(e);\r
575       }\r
576     });\r
577     PIDColour.setText("Percentage Identity");\r
578     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
579     {\r
580       public void actionPerformed(ActionEvent e)\r
581       {\r
582         PIDColour_actionPerformed(e);\r
583       }\r
584     });\r
585     BLOSUM62Colour.setText("BLOSUM62 Score");\r
586     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
587     {\r
588       public void actionPerformed(ActionEvent e)\r
589       {\r
590         BLOSUM62Colour_actionPerformed(e);\r
591       }\r
592     });\r
593     avDistanceTreeBlosumMenuItem.setText(\r
594         "Average Distance Using BLOSUM62");\r
595     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
596         ActionListener()\r
597     {\r
598       public void actionPerformed(ActionEvent e)\r
599       {\r
600         avTreeBlosumMenuItem_actionPerformed(e);\r
601       }\r
602     });\r
603     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
604     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
605     {\r
606       public void actionPerformed(ActionEvent e)\r
607       {\r
608         njTreeBlosumMenuItem_actionPerformed(e);\r
609       }\r
610     });\r
611     annotationPanelMenuItem.setActionCommand("");\r
612     annotationPanelMenuItem.setText("Show Annotations");\r
613     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
614     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
615     {\r
616       public void actionPerformed(ActionEvent e)\r
617       {\r
618         annotationPanelMenuItem_actionPerformed(e);\r
619       }\r
620     });\r
621     colourTextMenuItem.setText("Colour Text");\r
622     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
623     {\r
624       public void actionPerformed(ActionEvent e)\r
625       {\r
626         colourTextMenuItem_actionPerformed(e);\r
627       }\r
628     });\r
629     htmlMenuItem.setText("HTML");\r
630     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
631     {\r
632       public void actionPerformed(ActionEvent e)\r
633       {\r
634         htmlMenuItem_actionPerformed(e);\r
635       }\r
636     });\r
637     overviewMenuItem.setText("Overview Window");\r
638     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
639     {\r
640       public void actionPerformed(ActionEvent e)\r
641       {\r
642         overviewMenuItem_actionPerformed(e);\r
643       }\r
644     });\r
645     undoMenuItem.setEnabled(false);\r
646     undoMenuItem.setMnemonic('Z');\r
647     undoMenuItem.setText("Undo");\r
648     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
649         java.awt.event.KeyEvent.VK_Z,\r
650         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
651     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
652     {\r
653       public void actionPerformed(ActionEvent e)\r
654       {\r
655         undoMenuItem_actionPerformed(e);\r
656       }\r
657     });\r
658     redoMenuItem.setEnabled(false);\r
659     redoMenuItem.setMnemonic('0');\r
660     redoMenuItem.setText("Redo");\r
661     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
662     {\r
663       public void actionPerformed(ActionEvent e)\r
664       {\r
665         redoMenuItem_actionPerformed(e);\r
666       }\r
667     });\r
668     conservationMenuItem.setText("By Conservation");\r
669     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
670     {\r
671       public void actionPerformed(ActionEvent e)\r
672       {\r
673         conservationMenuItem_actionPerformed(e);\r
674       }\r
675     });\r
676     noColourmenuItem.setText("None");\r
677     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
678     {\r
679       public void actionPerformed(ActionEvent e)\r
680       {\r
681         noColourmenuItem_actionPerformed(e);\r
682       }\r
683     });\r
684     wrapMenuItem.setText("Wrap");\r
685     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
686     {\r
687       public void actionPerformed(ActionEvent e)\r
688       {\r
689         wrapMenuItem_actionPerformed(e);\r
690       }\r
691     });\r
692     printMenuItem.setText("Print");\r
693     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
694     {\r
695       public void actionPerformed(ActionEvent e)\r
696       {\r
697         printMenuItem_actionPerformed(e);\r
698       }\r
699     });\r
700     renderGapsMenuItem.setText("Show Gaps");\r
701     renderGapsMenuItem.setState(true);\r
702     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
703     {\r
704       public void actionPerformed(ActionEvent e)\r
705       {\r
706         renderGapsMenuItem_actionPerformed(e);\r
707       }\r
708     });\r
709     findMenuItem.setText("Find...");\r
710     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
711         java.awt.event.KeyEvent.VK_F,\r
712         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
713     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
714     {\r
715       public void actionPerformed(ActionEvent e)\r
716       {\r
717         findMenuItem_actionPerformed(e);\r
718       }\r
719     });\r
720     searchMenu.setText("Search");\r
721 \r
722     abovePIDThreshold.setText("Above Identity Threshold");\r
723     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
724     {\r
725       public void actionPerformed(ActionEvent e)\r
726       {\r
727         abovePIDThreshold_actionPerformed(e);\r
728       }\r
729     });\r
730     showSeqFeatures.setText("Show Sequence Features");\r
731     showSeqFeatures.addActionListener(new ActionListener()\r
732     {\r
733       public void actionPerformed(ActionEvent actionEvent)\r
734       {\r
735         showSeqFeatures_actionPerformed(actionEvent);\r
736       }\r
737     });\r
738     nucleotideColour.setText("Nucleotide");\r
739     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
740     {\r
741       public void actionPerformed(ActionEvent e)\r
742       {\r
743         nucleotideColour_actionPerformed(e);\r
744       }\r
745     });\r
746     deleteGroups.setText("Undefine groups");\r
747     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
748     {\r
749       public void actionPerformed(ActionEvent e)\r
750       {\r
751         deleteGroups_actionPerformed(e);\r
752       }\r
753     });\r
754     copy.setText("Copy");\r
755     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
756         java.awt.event.KeyEvent.VK_C,\r
757         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
758     copy.setMnemonic(KeyEvent.VK_C);\r
759 \r
760     copy.addActionListener(new java.awt.event.ActionListener()\r
761     {\r
762       public void actionPerformed(ActionEvent e)\r
763       {\r
764         copy_actionPerformed(e);\r
765       }\r
766     });\r
767     cut.setText("Cut");\r
768     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
769         java.awt.event.KeyEvent.VK_X,\r
770         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
771     cut.setMnemonic(KeyEvent.VK_X);\r
772     cut.addActionListener(new java.awt.event.ActionListener()\r
773     {\r
774       public void actionPerformed(ActionEvent e)\r
775       {\r
776         cut_actionPerformed(e);\r
777       }\r
778     });\r
779     delete.setText("Delete");\r
780     delete.addActionListener(new java.awt.event.ActionListener()\r
781     {\r
782       public void actionPerformed(ActionEvent e)\r
783       {\r
784         delete_actionPerformed(e);\r
785       }\r
786     });\r
787     jMenu1.setMnemonic('V');\r
788     jMenu1.setText("Paste");\r
789     pasteNew.setText("To New Alignment");\r
790     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
791         java.awt.event.KeyEvent.VK_V,\r
792         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
793     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
794     {\r
795       public void actionPerformed(ActionEvent e)\r
796       {\r
797         pasteNew_actionPerformed(e);\r
798       }\r
799     });\r
800     pasteThis.setText("Add To This Alignment");\r
801     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
802     {\r
803       public void actionPerformed(ActionEvent e)\r
804       {\r
805         pasteThis_actionPerformed(e);\r
806       }\r
807     });\r
808     applyToAllGroups.setText("Apply Colour To All Groups");\r
809     applyToAllGroups.setState(true);\r
810     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
811     {\r
812       public void actionPerformed(ActionEvent e)\r
813       {\r
814         applyToAllGroups_actionPerformed(e);\r
815       }\r
816     });\r
817     createPNG.addActionListener(new java.awt.event.ActionListener()\r
818     {\r
819       public void actionPerformed(ActionEvent e)\r
820       {\r
821         createPNG(null);\r
822       }\r
823     });\r
824     createPNG.setActionCommand("Save As PNG Image");\r
825     createPNG.setText("PNG");\r
826     font.setText("Font...");\r
827     font.addActionListener(new java.awt.event.ActionListener()\r
828     {\r
829       public void actionPerformed(ActionEvent e)\r
830       {\r
831         font_actionPerformed(e);\r
832       }\r
833     });\r
834 \r
835     seqLimits.setText("Show Sequence Limits");\r
836     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
837     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
838     {\r
839       public void actionPerformed(ActionEvent e)\r
840       {\r
841         seqLimit_actionPerformed(e);\r
842       }\r
843     });\r
844     epsFile.setText("EPS");\r
845     epsFile.addActionListener(new java.awt.event.ActionListener()\r
846     {\r
847       public void actionPerformed(ActionEvent e)\r
848       {\r
849         createEPS(null);\r
850       }\r
851     });\r
852     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
853     LoadtreeMenuItem.setText("Load Associated Tree");\r
854     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
855     {\r
856       public void actionPerformed(ActionEvent e)\r
857       {\r
858         LoadtreeMenuItem_actionPerformed(e);\r
859       }\r
860     });\r
861     scaleAbove.setVisible(false);\r
862     scaleAbove.setText("Scale Above");\r
863     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
864     {\r
865       public void actionPerformed(ActionEvent e)\r
866       {\r
867         scaleAbove_actionPerformed(e);\r
868       }\r
869     });\r
870     scaleLeft.setVisible(false);\r
871     scaleLeft.setSelected(true);\r
872     scaleLeft.setText("Scale Left");\r
873     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
874     {\r
875       public void actionPerformed(ActionEvent e)\r
876       {\r
877         scaleLeft_actionPerformed(e);\r
878       }\r
879     });\r
880     scaleRight.setVisible(false);\r
881     scaleRight.setSelected(true);\r
882     scaleRight.setText("Scale Right");\r
883     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
884     {\r
885       public void actionPerformed(ActionEvent e)\r
886       {\r
887         scaleRight_actionPerformed(e);\r
888       }\r
889     });\r
890     modifyPID.setText("Modify Identity Threshold...");\r
891     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
892     {\r
893       public void actionPerformed(ActionEvent e)\r
894       {\r
895         modifyPID_actionPerformed(e);\r
896       }\r
897     });\r
898     modifyConservation.setText("Modify Conservation Threshold...");\r
899     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
900     {\r
901       public void actionPerformed(ActionEvent e)\r
902       {\r
903         modifyConservation_actionPerformed(e);\r
904       }\r
905     });\r
906     sortByTreeMenu.setText("By Tree Order");\r
907     sort.setText("Sort");\r
908     calculate.setText("Calculate Tree");\r
909 \r
910     jMenu2.setText("Export");\r
911     padGapsMenuitem.setText("Pad Gaps");\r
912     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
913     padGapsMenuitem.addActionListener(new ActionListener()\r
914     {\r
915       public void actionPerformed(ActionEvent e)\r
916       {\r
917         padGapsMenuitem_actionPerformed(e);\r
918       }\r
919     });\r
920     vamsasStore.setVisible(false);\r
921     vamsasStore.setText("VAMSAS store");\r
922     vamsasStore.addActionListener(new ActionListener()\r
923     {\r
924       public void actionPerformed(ActionEvent e)\r
925       {\r
926         vamsasStore_actionPerformed(e);\r
927       }\r
928     });\r
929     showTranslation.setText("Translate cDNA");\r
930     showTranslation.addActionListener(new ActionListener()\r
931     {\r
932       public void actionPerformed(ActionEvent e)\r
933       {\r
934         showTranslation_actionPerformed(e);\r
935       }\r
936     });\r
937 \r
938    /* tabbedPane.addChangeListener(new ChangeListener()\r
939         {\r
940           public void stateChanged(ChangeEvent ece)\r
941           {\r
942 \r
943             tabSelected();\r
944           }\r
945         });*/\r
946     featureSettings.setText("Feature Settings...");\r
947     featureSettings.addActionListener(new ActionListener()\r
948     {\r
949       public void actionPerformed(ActionEvent e)\r
950       {\r
951         featureSettings_actionPerformed(e);\r
952       }\r
953     });\r
954     fetchSequence.setText("Fetch Sequence(s)...");\r
955     fetchSequence.addActionListener(new ActionListener()\r
956     {\r
957       public void actionPerformed(ActionEvent e)\r
958       {\r
959         fetchSequence_actionPerformed(e);\r
960       }\r
961     });\r
962     smoothFont.setText("Smooth Fonts");\r
963     smoothFont.addActionListener(new ActionListener()\r
964     {\r
965       public void actionPerformed(ActionEvent e)\r
966       {\r
967         smoothFont_actionPerformed(e);\r
968       }\r
969     });\r
970     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
971     annotationColour.setText("By Annotation...");\r
972     annotationColour.addActionListener(new ActionListener()\r
973     {\r
974       public void actionPerformed(ActionEvent e)\r
975       {\r
976         annotationColour_actionPerformed(e);\r
977       }\r
978     });\r
979     associatedData.setText("Load Features / Annotations");\r
980     associatedData.addActionListener(new ActionListener()\r
981     {\r
982       public void actionPerformed(ActionEvent e)\r
983       {\r
984         associatedData_actionPerformed(e);\r
985       }\r
986     });\r
987     autoCalculate.setText("Autocalculate Consensus");\r
988     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
989     autoCalculate.addActionListener(new ActionListener()\r
990     {\r
991       public void actionPerformed(ActionEvent e)\r
992       {\r
993         autoCalculate_actionPerformed(e);\r
994       }\r
995     });\r
996     addSequenceMenu.setText("Add Sequences");\r
997     addFromFile.setText("From File");\r
998     addFromFile.addActionListener(new ActionListener()\r
999     {\r
1000       public void actionPerformed(ActionEvent e)\r
1001       {\r
1002         addFromFile_actionPerformed(e);\r
1003       }\r
1004     });\r
1005     addFromText.setText("From Textbox");\r
1006     addFromText.addActionListener(new ActionListener()\r
1007     {\r
1008       public void actionPerformed(ActionEvent e)\r
1009       {\r
1010         addFromText_actionPerformed(e);\r
1011       }\r
1012     });\r
1013     addFromURL.setText("From URL");\r
1014     addFromURL.addActionListener(new ActionListener()\r
1015     {\r
1016       public void actionPerformed(ActionEvent e)\r
1017       {\r
1018         addFromURL_actionPerformed(e);\r
1019       }\r
1020     });\r
1021     exportFeatures.setText("Export Features...");\r
1022     exportFeatures.addActionListener(new ActionListener()\r
1023     {\r
1024       public void actionPerformed(ActionEvent e)\r
1025       {\r
1026         exportFeatures_actionPerformed(e);\r
1027       }\r
1028     });\r
1029     exportAnnotations.setText("Export Annotations...");\r
1030     exportAnnotations.addActionListener(new ActionListener()\r
1031     {\r
1032       public void actionPerformed(ActionEvent e)\r
1033       {\r
1034         exportAnnotations_actionPerformed(e);\r
1035       }\r
1036     });\r
1037     statusPanel.setLayout(gridLayout1);\r
1038     jMenu3.setText("Show");\r
1039     showAllSeqs.setText("All Sequences");\r
1040     showAllSeqs.addActionListener(new ActionListener()\r
1041     {\r
1042       public void actionPerformed(ActionEvent e)\r
1043       {\r
1044         showAllSeqs_actionPerformed(e);\r
1045       }\r
1046     });\r
1047     showAllColumns.setText("All Columns");\r
1048     showAllColumns.addActionListener(new ActionListener()\r
1049     {\r
1050       public void actionPerformed(ActionEvent e)\r
1051       {\r
1052         showAllColumns_actionPerformed(e);\r
1053       }\r
1054     });\r
1055     jMenu4.setText("Hide");\r
1056     hideSelSequences.setText("Selected Sequences");\r
1057     hideSelSequences.addActionListener(new ActionListener()\r
1058     {\r
1059       public void actionPerformed(ActionEvent e)\r
1060       {\r
1061         hideSelSequences_actionPerformed(e);\r
1062       }\r
1063     });\r
1064     hideSelColumns.setText("Selected Columns");\r
1065     hideSelColumns.addActionListener(new ActionListener()\r
1066     {\r
1067       public void actionPerformed(ActionEvent e)\r
1068       {\r
1069         hideSelColumns_actionPerformed(e);\r
1070       }\r
1071     });\r
1072     hiddenMarkers.setText("Hidden Markers");\r
1073     hiddenMarkers.setState(true);\r
1074     hiddenMarkers.addActionListener(new ActionListener()\r
1075     {\r
1076       public void actionPerformed(ActionEvent e)\r
1077       {\r
1078         hiddenMarkers_actionPerformed(e);\r
1079       }\r
1080     });\r
1081     invertColSel.setText("Invert Column Selection");\r
1082     invertColSel.addActionListener(new ActionListener()\r
1083     {\r
1084       public void actionPerformed(ActionEvent e)\r
1085       {\r
1086         invertColSel_actionPerformed(e);\r
1087       }\r
1088     });\r
1089 \r
1090     alignFrameMenuBar.add(fileMenu);\r
1091     alignFrameMenuBar.add(editMenu);\r
1092     alignFrameMenuBar.add(searchMenu);\r
1093     alignFrameMenuBar.add(viewMenu);\r
1094     alignFrameMenuBar.add(colourMenu);\r
1095     alignFrameMenuBar.add(calculateMenu);\r
1096     alignFrameMenuBar.add(webService);\r
1097     fileMenu.add(addSequenceMenu);\r
1098     fileMenu.add(fetchSequence);\r
1099     fileMenu.addSeparator();\r
1100     fileMenu.add(vamsasStore);\r
1101     fileMenu.add(saveAlignmentMenu);\r
1102     fileMenu.add(jMenu2);\r
1103     fileMenu.add(outputTextboxMenu);\r
1104     fileMenu.add(printMenuItem);\r
1105     fileMenu.addSeparator();\r
1106     fileMenu.add(exportFeatures);\r
1107     fileMenu.add(exportAnnotations);\r
1108     fileMenu.add(LoadtreeMenuItem);\r
1109     fileMenu.add(associatedData);\r
1110     fileMenu.addSeparator();\r
1111     fileMenu.add(closeMenuItem);\r
1112     editMenu.add(undoMenuItem);\r
1113     editMenu.add(redoMenuItem);\r
1114     editMenu.add(cut);\r
1115     editMenu.add(copy);\r
1116     editMenu.add(jMenu1);\r
1117     editMenu.add(delete);\r
1118     editMenu.addSeparator();\r
1119     editMenu.add(selectAllSequenceMenuItem);\r
1120     editMenu.add(deselectAllSequenceMenuItem);\r
1121     editMenu.add(invertSequenceMenuItem);\r
1122     editMenu.add(invertColSel);\r
1123     editMenu.add(deleteGroups);\r
1124     editMenu.addSeparator();\r
1125     editMenu.add(remove2LeftMenuItem);\r
1126     editMenu.add(remove2RightMenuItem);\r
1127     editMenu.add(removeGappedColumnMenuItem);\r
1128     editMenu.add(removeAllGapsMenuItem);\r
1129     editMenu.add(removeRedundancyMenuItem);\r
1130     editMenu.addSeparator();\r
1131     editMenu.add(padGapsMenuitem);\r
1132     searchMenu.add(findMenuItem);\r
1133     viewMenu.add(font);\r
1134     viewMenu.add(smoothFont);\r
1135     viewMenu.addSeparator();\r
1136     viewMenu.add(jMenu3);\r
1137     viewMenu.add(jMenu4);\r
1138     viewMenu.add(hiddenMarkers);\r
1139     viewMenu.addSeparator();\r
1140     viewMenu.add(wrapMenuItem);\r
1141     viewMenu.add(seqLimits);\r
1142     viewMenu.add(scaleAbove);\r
1143     viewMenu.add(scaleLeft);\r
1144     viewMenu.add(scaleRight);\r
1145     viewMenu.add(viewBoxesMenuItem);\r
1146     viewMenu.add(viewTextMenuItem);\r
1147     viewMenu.add(colourTextMenuItem);\r
1148     viewMenu.add(renderGapsMenuItem);\r
1149     viewMenu.add(annotationPanelMenuItem);\r
1150     viewMenu.addSeparator();\r
1151     viewMenu.add(showSeqFeatures);\r
1152     viewMenu.add(featureSettings);\r
1153     viewMenu.addSeparator();\r
1154     viewMenu.add(overviewMenuItem);\r
1155     colourMenu.add(applyToAllGroups);\r
1156     colourMenu.addSeparator();\r
1157     colourMenu.add(noColourmenuItem);\r
1158     colourMenu.add(clustalColour);\r
1159     colourMenu.add(BLOSUM62Colour);\r
1160     colourMenu.add(PIDColour);\r
1161     colourMenu.add(zappoColour);\r
1162     colourMenu.add(taylorColour);\r
1163     colourMenu.add(hydrophobicityColour);\r
1164     colourMenu.add(helixColour);\r
1165     colourMenu.add(strandColour);\r
1166     colourMenu.add(turnColour);\r
1167     colourMenu.add(buriedColour);\r
1168     colourMenu.add(nucleotideColour);\r
1169     colourMenu.add(userDefinedColour);\r
1170     colourMenu.addSeparator();\r
1171     colourMenu.add(conservationMenuItem);\r
1172     colourMenu.add(modifyConservation);\r
1173     colourMenu.add(abovePIDThreshold);\r
1174     colourMenu.add(modifyPID);\r
1175     colourMenu.add(annotationColour);\r
1176     calculateMenu.add(sort);\r
1177     calculateMenu.add(calculate);\r
1178     calculateMenu.addSeparator();\r
1179     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1180     calculateMenu.add(PCAMenuItem);\r
1181     calculateMenu.addSeparator();\r
1182     calculateMenu.add(showTranslation);\r
1183     calculateMenu.add(autoCalculate);\r
1184     webServiceNoServices=new JMenuItem("<No Services>");\r
1185     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1186     jMenu1.add(pasteThis);\r
1187     sort.add(sortIDMenuItem);\r
1188     sort.add(sortGroupMenuItem);\r
1189     sort.add(sortPairwiseMenuItem);\r
1190     calculate.add(averageDistanceTreeMenuItem);\r
1191     calculate.add(neighbourTreeMenuItem);\r
1192     calculate.add(avDistanceTreeBlosumMenuItem);\r
1193     calculate.add(njTreeBlosumMenuItem);\r
1194     jMenu2.add(htmlMenuItem);\r
1195     jMenu2.add(epsFile);\r
1196     jMenu2.add(createPNG);\r
1197     addSequenceMenu.add(addFromFile);\r
1198     addSequenceMenu.add(addFromText);\r
1199     addSequenceMenu.add(addFromURL);\r
1200     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1201     statusPanel.add(statusBar, null);\r
1202     jMenu3.add(showAllColumns);\r
1203     jMenu3.add(showAllSeqs);\r
1204     jMenu4.add(hideSelColumns);\r
1205     jMenu4.add(hideSelSequences);\r
1206   }\r
1207 \r
1208   protected void outputText_actionPerformed(ActionEvent e)\r
1209   {\r
1210   }\r
1211 \r
1212   public void addFromFile_actionPerformed(ActionEvent e)\r
1213   {\r
1214 \r
1215   }\r
1216 \r
1217   public void addFromText_actionPerformed(ActionEvent e)\r
1218   {\r
1219 \r
1220   }\r
1221 \r
1222   public void addFromURL_actionPerformed(ActionEvent e)\r
1223   {\r
1224 \r
1225   }\r
1226 \r
1227   public void exportFeatures_actionPerformed(ActionEvent e)\r
1228   {\r
1229 \r
1230   }\r
1231 \r
1232   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1233   {\r
1234 \r
1235   }\r
1236 \r
1237   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1238   {\r
1239   }\r
1240 \r
1241   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1242   {\r
1243   }\r
1244 \r
1245   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1246   {\r
1247   }\r
1248 \r
1249   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1250   {\r
1251   }\r
1252 \r
1253   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1254   {\r
1255   }\r
1256 \r
1257   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1258   {\r
1259   }\r
1260 \r
1261   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1262   {\r
1263   }\r
1264 \r
1265   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1266   {\r
1267   }\r
1268 \r
1269   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1270   {\r
1271   }\r
1272 \r
1273   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1274   {\r
1275   }\r
1276 \r
1277   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1278   {\r
1279   }\r
1280 \r
1281   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1282   {\r
1283   }\r
1284 \r
1285   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1286   {\r
1287   }\r
1288 \r
1289   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1290   {\r
1291   }\r
1292 \r
1293   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1294   {\r
1295   }\r
1296 \r
1297   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1298   {\r
1299   }\r
1300 \r
1301   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1302   {\r
1303   }\r
1304 \r
1305   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1306   {\r
1307   }\r
1308 \r
1309   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1310   {\r
1311   }\r
1312 \r
1313   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1314   {\r
1315   }\r
1316 \r
1317   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1318   {\r
1319   }\r
1320 \r
1321   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1322   {\r
1323   }\r
1324 \r
1325   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1326   {\r
1327   }\r
1328 \r
1329   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1330   {\r
1331   }\r
1332 \r
1333   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1334   {\r
1335   }\r
1336 \r
1337   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1338   {\r
1339   }\r
1340 \r
1341   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1342   {\r
1343   }\r
1344 \r
1345   protected void clustalColour_actionPerformed(ActionEvent e)\r
1346   {\r
1347   }\r
1348 \r
1349   protected void zappoColour_actionPerformed(ActionEvent e)\r
1350   {\r
1351   }\r
1352 \r
1353   protected void taylorColour_actionPerformed(ActionEvent e)\r
1354   {\r
1355   }\r
1356 \r
1357   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1358   {\r
1359   }\r
1360 \r
1361   protected void helixColour_actionPerformed(ActionEvent e)\r
1362   {\r
1363   }\r
1364 \r
1365   protected void strandColour_actionPerformed(ActionEvent e)\r
1366   {\r
1367   }\r
1368 \r
1369   protected void turnColour_actionPerformed(ActionEvent e)\r
1370   {\r
1371   }\r
1372 \r
1373   protected void buriedColour_actionPerformed(ActionEvent e)\r
1374   {\r
1375   }\r
1376 \r
1377   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1378   {\r
1379   }\r
1380 \r
1381   protected void PIDColour_actionPerformed(ActionEvent e)\r
1382   {\r
1383   }\r
1384 \r
1385   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1386   {\r
1387   }\r
1388 \r
1389   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1390   {\r
1391   }\r
1392 \r
1393   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1394   {\r
1395   }\r
1396 \r
1397   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1398   {\r
1399   }\r
1400 \r
1401   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1402   {\r
1403   }\r
1404 \r
1405   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1406   {\r
1407   }\r
1408 \r
1409   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1410   {\r
1411   }\r
1412 \r
1413   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1414   {\r
1415   }\r
1416 \r
1417   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1418   {\r
1419   }\r
1420 \r
1421   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1422   {\r
1423   }\r
1424 \r
1425   protected void copy_actionPerformed(ActionEvent e)\r
1426   {\r
1427   }\r
1428 \r
1429   protected void cut_actionPerformed(ActionEvent e)\r
1430   {\r
1431   }\r
1432 \r
1433   protected void delete_actionPerformed(ActionEvent e)\r
1434   {\r
1435   }\r
1436 \r
1437   protected void pasteNew_actionPerformed(ActionEvent e)\r
1438   {\r
1439   }\r
1440 \r
1441   protected void pasteThis_actionPerformed(ActionEvent e)\r
1442   {\r
1443   }\r
1444 \r
1445   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1446   {\r
1447   }\r
1448 \r
1449   public void createPNG(java.io.File f)\r
1450   {\r
1451   }\r
1452 \r
1453   protected void font_actionPerformed(ActionEvent e)\r
1454   {\r
1455   }\r
1456 \r
1457   protected void seqLimit_actionPerformed(ActionEvent e)\r
1458   {\r
1459   }\r
1460 \r
1461   public void seqDBRef_actionPerformed(ActionEvent e)\r
1462   {\r
1463 \r
1464   }\r
1465 \r
1466 \r
1467   public void createEPS(java.io.File f)\r
1468   {\r
1469   }\r
1470 \r
1471   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1472   {\r
1473   }\r
1474 \r
1475   protected void jpred_actionPerformed(ActionEvent e)\r
1476   {\r
1477   }\r
1478 \r
1479   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1480   {\r
1481   }\r
1482 \r
1483   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1484   {\r
1485   }\r
1486 \r
1487   protected void scaleRight_actionPerformed(ActionEvent e)\r
1488   {\r
1489   }\r
1490 \r
1491   protected void modifyPID_actionPerformed(ActionEvent e)\r
1492   {\r
1493   }\r
1494 \r
1495   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1496   {\r
1497   }\r
1498 \r
1499 \r
1500 \r
1501   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1502   {\r
1503   }\r
1504 \r
1505   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1506   {\r
1507   }\r
1508 \r
1509 \r
1510   public void vamsasStore_actionPerformed(ActionEvent e)\r
1511   {\r
1512 \r
1513   }\r
1514 \r
1515   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1516   {\r
1517 \r
1518   }\r
1519 \r
1520   public void showTranslation_actionPerformed(ActionEvent e)\r
1521   {\r
1522 \r
1523   }\r
1524 \r
1525   public void featureSettings_actionPerformed(ActionEvent e)\r
1526   {\r
1527 \r
1528   }\r
1529 \r
1530   public void fetchSequence_actionPerformed(ActionEvent e)\r
1531   {\r
1532 \r
1533   }\r
1534 \r
1535   public void smoothFont_actionPerformed(ActionEvent e)\r
1536   {\r
1537 \r
1538   }\r
1539 \r
1540   public void annotationColour_actionPerformed(ActionEvent e)\r
1541   {\r
1542 \r
1543   }\r
1544 \r
1545 \r
1546   public void associatedData_actionPerformed(ActionEvent e)\r
1547   {\r
1548 \r
1549   }\r
1550 \r
1551   public void autoCalculate_actionPerformed(ActionEvent e)\r
1552   {\r
1553 \r
1554   }\r
1555 \r
1556   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1557   {\r
1558 \r
1559   }\r
1560 \r
1561   public void showAllColumns_actionPerformed(ActionEvent e)\r
1562   {\r
1563 \r
1564   }\r
1565 \r
1566   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1567   {\r
1568 \r
1569   }\r
1570 \r
1571   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1572   {\r
1573 \r
1574   }\r
1575 \r
1576   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1577   {\r
1578 \r
1579   }\r
1580 \r
1581   public void findPdbId_actionPerformed(ActionEvent e)\r
1582   {\r
1583 \r
1584   }\r
1585 \r
1586   public void enterPdbId_actionPerformed(ActionEvent e)\r
1587   {\r
1588 \r
1589   }\r
1590 \r
1591   public void pdbFile_actionPerformed(ActionEvent e)\r
1592   {\r
1593 \r
1594   }\r
1595 \r
1596   public void invertColSel_actionPerformed(ActionEvent e)\r
1597   {\r
1598 \r
1599   }\r
1600 }\r