Destroy Alignment when closing frame
[jalview.git] / src / jalview / jbgui / GPreferences.java
1 /*\r
2  * Jalview - A Sequence Alignment Editor and Viewer\r
3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
4  *\r
5  * This program is free software; you can redistribute it and/or\r
6  * modify it under the terms of the GNU General Public License\r
7  * as published by the Free Software Foundation; either version 2\r
8  * of the License, or (at your option) any later version.\r
9  *\r
10  * This program is distributed in the hope that it will be useful,\r
11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
13  * GNU General Public License for more details.\r
14  *\r
15  * You should have received a copy of the GNU General Public License\r
16  * along with this program; if not, write to the Free Software\r
17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
18  */\r
19 package jalview.jbgui;\r
20 \r
21 import java.awt.*;\r
22 import java.awt.event.*;\r
23 import javax.swing.*;\r
24 import javax.swing.border.*;\r
25 import javax.swing.event.*;\r
26 import java.awt.Rectangle;\r
27 \r
28 /**\r
29  * DOCUMENT ME!\r
30  *\r
31  * @author $author$\r
32  * @version $Revision$\r
33  */\r
34 public class GPreferences\r
35     extends JPanel\r
36 {\r
37   JTabbedPane tabbedPane = new JTabbedPane();\r
38 \r
39   JButton ok = new JButton();\r
40   JButton cancel = new JButton();\r
41   JPanel okCancelPanel = new JPanel();\r
42   BorderLayout borderLayout1 = new BorderLayout();\r
43   protected JCheckBox quality = new JCheckBox();\r
44   JPanel visualTab = new JPanel();\r
45   protected JCheckBox fullScreen = new JCheckBox();\r
46   protected JCheckBox conservation = new JCheckBox();\r
47   protected JCheckBox identity = new JCheckBox();\r
48   protected JCheckBox annotations = new JCheckBox();\r
49   JLabel gapLabel = new JLabel();\r
50   protected JComboBox colour = new JComboBox();\r
51   JLabel colourLabel = new JLabel();\r
52   JLabel fontLabel = new JLabel();\r
53   protected JComboBox fontSizeCB = new JComboBox();\r
54   protected JComboBox fontStyleCB = new JComboBox();\r
55   protected JComboBox fontNameCB = new JComboBox();\r
56   protected JComboBox gapSymbolCB = new JComboBox();\r
57   protected JCheckBox startupCheckbox = new JCheckBox();\r
58   protected JTextField startupFileTextfield = new JTextField();\r
59   JPanel connectTab = new JPanel();\r
60   JLabel serverLabel = new JLabel();\r
61   protected JList linkURLList = new JList();\r
62   protected JTextField proxyServerTB = new JTextField();\r
63   protected JTextField proxyPortTB = new JTextField();\r
64   JLabel portLabel = new JLabel();\r
65   JLabel browserLabel = new JLabel();\r
66   protected JTextField defaultBrowser = new JTextField();\r
67   JButton newLink = new JButton();\r
68   JButton editLink = new JButton();\r
69   JButton deleteLink = new JButton();\r
70   JScrollPane linkScrollPane = new JScrollPane();\r
71   JPanel linkPanel = new JPanel();\r
72   BorderLayout borderLayout2 = new BorderLayout();\r
73   JPanel editLinkButtons = new JPanel();\r
74   GridLayout gridLayout1 = new GridLayout();\r
75   protected JList linkNameList = new JList();\r
76   JPanel linkPanel2 = new JPanel();\r
77   BorderLayout borderLayout3 = new BorderLayout();\r
78   protected JCheckBox useProxy = new JCheckBox();\r
79   JPanel jPanel1 = new JPanel();\r
80   TitledBorder titledBorder1 = new TitledBorder("Proxy Server");\r
81   TitledBorder titledBorder2 = new TitledBorder("File Output");\r
82   GridBagLayout gridBagLayout2 = new GridBagLayout();\r
83   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
84   GridBagLayout gridBagLayout3 = new GridBagLayout();\r
85   protected JComboBox sortby = new JComboBox();\r
86   JLabel sortLabel = new JLabel();\r
87   JPanel jPanel2 = new JPanel();\r
88   GridLayout gridLayout2 = new GridLayout();\r
89   JPanel jPanel3 = new JPanel();\r
90   JPanel exportTab = new JPanel();\r
91   JLabel epsLabel = new JLabel();\r
92   protected JComboBox epsRendering = new JComboBox();\r
93   JLabel jLabel1 = new JLabel();\r
94   protected JCheckBox blcjv = new JCheckBox();\r
95   protected JCheckBox pileupjv = new JCheckBox();\r
96   protected JCheckBox clustaljv = new JCheckBox();\r
97   protected JCheckBox msfjv = new JCheckBox();\r
98   protected JCheckBox fastajv = new JCheckBox();\r
99   protected JCheckBox pfamjv = new JCheckBox();\r
100   FlowLayout flowLayout1 = new FlowLayout();\r
101   protected JCheckBox pirjv = new JCheckBox();\r
102   JPanel jPanel11 = new JPanel();\r
103   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
104   protected JCheckBox seqLimit = new JCheckBox();\r
105   GridLayout gridLayout3 = new GridLayout();\r
106   protected JCheckBox smoothFont = new JCheckBox();\r
107   JPanel calcTab = new JPanel();\r
108   protected JCheckBox autoCalculateConsCheck = new JCheckBox();\r
109   protected JCheckBox padGaps = new JCheckBox();\r
110   protected JCheckBox modellerOutput = new JCheckBox();\r
111   protected JPanel dasPanel = new JPanel();\r
112   BorderLayout borderLayout4 = new BorderLayout();\r
113   protected JCheckBox wrap = new JCheckBox();\r
114   protected JCheckBox rightAlign = new JCheckBox();\r
115   protected JCheckBox idItalics = new JCheckBox();\r
116   protected JCheckBox openoverv = new JCheckBox();\r
117   /**\r
118    * Creates a new GPreferences object.\r
119    */\r
120   public GPreferences()\r
121   {\r
122     try\r
123     {\r
124       jbInit();\r
125     }\r
126     catch (Exception ex)\r
127     {\r
128       ex.printStackTrace();\r
129     }\r
130   }\r
131 \r
132   /**\r
133    * DOCUMENT ME!\r
134    *\r
135    * @throws Exception DOCUMENT ME!\r
136    */\r
137   private void jbInit()\r
138       throws Exception\r
139   {\r
140     this.setLayout(borderLayout1);\r
141     ok.setText("OK");\r
142     ok.addActionListener(new ActionListener()\r
143     {\r
144       public void actionPerformed(ActionEvent e)\r
145       {\r
146         ok_actionPerformed(e);\r
147       }\r
148     });\r
149     cancel.setText("Cancel");\r
150     cancel.addActionListener(new ActionListener()\r
151     {\r
152       public void actionPerformed(ActionEvent e)\r
153       {\r
154         cancel_actionPerformed(e);\r
155       }\r
156     });\r
157     quality.setEnabled(false);\r
158     quality.setFont(verdana11);\r
159     quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
160     quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
161     quality.setSelected(true);\r
162     quality.setText("Quality");\r
163     visualTab.setBorder(new TitledBorder("Open new alignment"));\r
164     visualTab.setLayout(null);\r
165     fullScreen.setFont(verdana11);\r
166     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
167     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
168     fullScreen.setText("Maximise Window");\r
169     conservation.setEnabled(false);\r
170     conservation.setFont(verdana11);\r
171     conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
172     conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
173     conservation.setSelected(true);\r
174     conservation.setText("Conservation");\r
175     identity.setEnabled(false);\r
176     identity.setFont(verdana11);\r
177     identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
178     identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
179     identity.setSelected(true);\r
180     identity.setText("Consensus");\r
181     annotations.setFont(verdana11);\r
182     annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
183     annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
184     annotations.setSelected(true);\r
185     annotations.setText("Show Annotations");\r
186     annotations.addActionListener(new ActionListener()\r
187     {\r
188       public void actionPerformed(ActionEvent e)\r
189       {\r
190         annotations_actionPerformed(e);\r
191       }\r
192     });\r
193     gapLabel.setFont(verdana11);\r
194     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
195     gapLabel.setText("Gap Symbol ");\r
196     colour.setFont(verdana11);\r
197     colour.setBounds(new Rectangle(172, 225, 155, 21));\r
198     colourLabel.setFont(verdana11);\r
199     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
200     colourLabel.setText("Colour ");\r
201     fontLabel.setFont(verdana11);\r
202     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
203     fontLabel.setText("Font ");\r
204     fontSizeCB.setFont(verdana11);\r
205     fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21));\r
206     fontStyleCB.setFont(verdana11);\r
207     fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));\r
208     fontNameCB.setFont(verdana11);\r
209     fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));\r
210     gapSymbolCB.setFont(verdana11);\r
211     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));\r
212     startupCheckbox.setText("Open file");\r
213     startupCheckbox.setFont(verdana11);\r
214     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
215     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
216     startupCheckbox.setSelected(true);\r
217     startupFileTextfield.setFont(verdana11);\r
218     startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));\r
219     startupFileTextfield.addMouseListener(new MouseAdapter()\r
220     {\r
221       public void mouseClicked(MouseEvent e)\r
222       {\r
223         if (e.getClickCount() > 1)\r
224         {\r
225           startupFileTextfield_mouseClicked();\r
226         }\r
227       }\r
228     });\r
229 \r
230     connectTab.setLayout(gridBagLayout3);\r
231     serverLabel.setText("Address");\r
232     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
233     serverLabel.setFont(verdana11);\r
234     proxyServerTB.setFont(verdana11);\r
235     proxyPortTB.setFont(verdana11);\r
236     portLabel.setFont(verdana11);\r
237     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
238     portLabel.setText("Port");\r
239     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));\r
240     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);\r
241     browserLabel.setText("Default Browser (Unix)");\r
242     defaultBrowser.setFont(verdana11);\r
243     defaultBrowser.setText("");\r
244     newLink.setText("New");\r
245     newLink.addActionListener(new java.awt.event.ActionListener()\r
246     {\r
247       public void actionPerformed(ActionEvent e)\r
248       {\r
249         newLink_actionPerformed(e);\r
250       }\r
251     });\r
252     editLink.setText("Edit");\r
253     editLink.addActionListener(new java.awt.event.ActionListener()\r
254     {\r
255       public void actionPerformed(ActionEvent e)\r
256       {\r
257         editLink_actionPerformed(e);\r
258       }\r
259     });\r
260     deleteLink.setText("Delete");\r
261     deleteLink.addActionListener(new java.awt.event.ActionListener()\r
262     {\r
263       public void actionPerformed(ActionEvent e)\r
264       {\r
265         deleteLink_actionPerformed(e);\r
266       }\r
267     });\r
268 \r
269     linkURLList.addListSelectionListener(new ListSelectionListener()\r
270     {\r
271       public void valueChanged(ListSelectionEvent e)\r
272       {\r
273         int index = linkURLList.getSelectedIndex();\r
274         linkNameList.setSelectedIndex(index);\r
275       }\r
276     });\r
277 \r
278     linkNameList.addListSelectionListener(new ListSelectionListener()\r
279     {\r
280       public void valueChanged(ListSelectionEvent e)\r
281       {\r
282         int index = linkNameList.getSelectedIndex();\r
283         linkURLList.setSelectedIndex(index);\r
284       }\r
285     });\r
286 \r
287     linkScrollPane.setBorder(null);\r
288     linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));\r
289     linkPanel.setLayout(borderLayout2);\r
290     editLinkButtons.setLayout(gridLayout1);\r
291     gridLayout1.setRows(3);\r
292     linkNameList.setFont(verdana11);\r
293     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
294     linkPanel2.setLayout(borderLayout3);\r
295     linkURLList.setFont(verdana11);\r
296     linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
297 \r
298     defaultBrowser.addMouseListener(new MouseAdapter()\r
299     {\r
300       public void mouseClicked(MouseEvent e)\r
301       {\r
302         if (e.getClickCount() > 1)\r
303         {\r
304           defaultBrowser_mouseClicked(e);\r
305         }\r
306       }\r
307     });\r
308     useProxy.setFont(verdana11);\r
309     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);\r
310     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);\r
311     useProxy.setText("Use a proxy server");\r
312     useProxy.addActionListener(new ActionListener()\r
313     {\r
314       public void actionPerformed(ActionEvent e)\r
315       {\r
316         useProxy_actionPerformed();\r
317       }\r
318     });\r
319     jPanel1.setBorder(titledBorder1);\r
320     jPanel1.setLayout(gridBagLayout1);\r
321     sortby.setFont(verdana11);\r
322     sortby.setBounds(new Rectangle(172, 249, 155, 21));\r
323     sortLabel.setFont(verdana11);\r
324     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
325     sortLabel.setText("Sort by ");\r
326     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));\r
327     jPanel2.setLayout(gridLayout2);\r
328     gridLayout2.setRows(12);\r
329     jPanel3.setBounds(new Rectangle(173, 35, 274, 26));\r
330     exportTab.setLayout(null);\r
331     epsLabel.setFont(verdana11);\r
332     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
333     epsLabel.setText("EPS Rendering Style");\r
334     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));\r
335     epsRendering.setFont(verdana11);\r
336     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));\r
337     jLabel1.setFont(verdana11);\r
338     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
339     jLabel1.setText("Append /start-end (/15-380)");\r
340     jLabel1.setFont(verdana11);\r
341     fastajv.setFont(verdana11);\r
342     fastajv.setHorizontalAlignment(SwingConstants.LEFT);\r
343     clustaljv.setText("Clustal     ");\r
344     blcjv.setText("BLC     ");\r
345     fastajv.setText("Fasta     ");\r
346     msfjv.setText("MSF     ");\r
347     pfamjv.setText("PFAM     ");\r
348     pileupjv.setText("Pileup     ");\r
349     msfjv.setFont(verdana11);\r
350     msfjv.setHorizontalAlignment(SwingConstants.LEFT);\r
351     pirjv.setText("PIR     ");\r
352     jPanel11.setFont(verdana11);\r
353     jPanel11.setBorder(titledBorder2);\r
354     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));\r
355     jPanel11.setLayout(gridLayout3);\r
356     blcjv.setFont(verdana11);\r
357     blcjv.setHorizontalAlignment(SwingConstants.LEFT);\r
358     clustaljv.setFont(verdana11);\r
359     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);\r
360     pfamjv.setFont(verdana11);\r
361     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);\r
362     pileupjv.setFont(verdana11);\r
363     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);\r
364     pirjv.setFont(verdana11);\r
365     pirjv.setHorizontalAlignment(SwingConstants.LEFT);\r
366     seqLimit.setFont(verdana11);\r
367     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);\r
368     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);\r
369     seqLimit.setText("Full Sequence Id");\r
370     gridLayout3.setRows(8);\r
371     smoothFont.setFont(verdana11);\r
372     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);\r
373     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);\r
374     smoothFont.setText("Smooth Font");\r
375     calcTab.setLayout(null);\r
376     autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
377     autoCalculateConsCheck.setText("AutoCalculate Consensus");\r
378     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));\r
379     padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
380     padGaps.setText("Pad gaps when editing");\r
381     padGaps.setBounds(new Rectangle(22, 94, 168, 23));\r
382     modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
383     modellerOutput.setText("Use Modeller Output");\r
384     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));\r
385     dasPanel.setLayout(borderLayout4);\r
386     wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
387     wrap.setHorizontalAlignment(SwingConstants.TRAILING);\r
388     wrap.setHorizontalTextPosition(SwingConstants.LEADING);\r
389     wrap.setText("Wrap Alignment");\r
390     rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
391     rightAlign.setForeground(Color.black);\r
392     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);\r
393     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);\r
394     rightAlign.setText("Right Align Ids");\r
395     idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
396     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);\r
397     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);\r
398     idItalics.setText("Sequence Name Italics");\r
399     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
400     openoverv.setActionCommand("Open Overview");\r
401     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);\r
402     openoverv.setHorizontalTextPosition(SwingConstants.LEADING);\r
403     openoverv.setText("Open Overview Window");\r
404     openoverv.setBounds(new Rectangle(169, 17, 200, 23));\r
405     jPanel2.add(fullScreen);\r
406     jPanel2.add(annotations);\r
407     jPanel2.add(seqLimit);\r
408     jPanel2.add(rightAlign);\r
409     jPanel2.add(fontLabel);\r
410     jPanel2.add(idItalics);\r
411     jPanel2.add(smoothFont);\r
412     jPanel2.add(wrap);\r
413     jPanel2.add(gapLabel);\r
414     jPanel2.add(colourLabel);\r
415     jPanel2.add(sortLabel);\r
416     jPanel2.add(startupCheckbox);\r
417     visualTab.add(openoverv);\r
418     visualTab.add(startupFileTextfield);\r
419     visualTab.add(sortby);\r
420     visualTab.add(colour);\r
421     visualTab.add(gapSymbolCB);\r
422     visualTab.add(jPanel3);\r
423     visualTab.add(fontNameCB);\r
424     visualTab.add(fontSizeCB);\r
425     visualTab.add(fontStyleCB);\r
426     jPanel3.add(conservation);\r
427     jPanel3.add(identity);\r
428     jPanel3.add(quality);\r
429     visualTab.add(jPanel2);\r
430     linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
431     editLinkButtons.add(newLink, null);\r
432     editLinkButtons.add(editLink, null);\r
433     editLinkButtons.add(deleteLink, null);\r
434     linkPanel.add(linkScrollPane, BorderLayout.CENTER);\r
435     linkScrollPane.getViewport().add(linkPanel2, null);\r
436     linkPanel2.add(linkURLList, BorderLayout.CENTER);\r
437     linkPanel2.add(linkNameList, BorderLayout.WEST);\r
438     okCancelPanel.add(ok);\r
439     okCancelPanel.add(cancel);\r
440     this.add(tabbedPane, java.awt.BorderLayout.CENTER);\r
441 \r
442     this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);\r
443     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
444         , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
445         new Insets(0, 2, 4, 0), 5, 0));\r
446     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0\r
447                                                   , GridBagConstraints.WEST,\r
448                                                   GridBagConstraints.NONE,\r
449                                                   new Insets(0, 0, 4, 0), 11, 6));\r
450     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0\r
451         , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
452         new Insets(16, 0, 0, 12), 359, -17));\r
453     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
454         , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
455         new Insets(21, 0, 35, 12), 4, 6));\r
456     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
457         , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
458         new Insets(16, 0, 0, 0), 5, 1));\r
459     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0\r
460         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
461         new Insets(0, 2, 4, 2), 54, 1));\r
462     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
463         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
464         new Insets(0, 2, 4, 0), 263, 1));\r
465     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
466         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
467         new Insets(15, 0, 0, 15), 307, 1));\r
468 \r
469     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
470                                                  , GridBagConstraints.WEST,\r
471                                                  GridBagConstraints.NONE,\r
472                                                  new Insets(0, 2, 5, 185), 2,\r
473                                                  -4));\r
474     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();\r
475     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
476     gapSymbolCB.setRenderer(dlcr);\r
477 \r
478     tabbedPane.add(visualTab, "Visual");\r
479     tabbedPane.add(connectTab, "Connections");\r
480     tabbedPane.add(exportTab, "Output");\r
481     jPanel11.add(jLabel1);\r
482     jPanel11.add(blcjv);\r
483     jPanel11.add(clustaljv);\r
484     jPanel11.add(fastajv);\r
485     jPanel11.add(msfjv);\r
486     jPanel11.add(pfamjv);\r
487     jPanel11.add(pileupjv);\r
488     jPanel11.add(pirjv);\r
489     exportTab.add(modellerOutput);\r
490     tabbedPane.add(calcTab, "Editing");\r
491     calcTab.add(autoCalculateConsCheck);\r
492     calcTab.add(padGaps);\r
493     tabbedPane.add(dasPanel, "DAS Settings");\r
494 \r
495     exportTab.add(epsLabel);\r
496     exportTab.add(epsRendering);\r
497     exportTab.add(jPanel11);\r
498   }\r
499 \r
500   /**\r
501    * DOCUMENT ME!\r
502    *\r
503    * @param e DOCUMENT ME!\r
504    */\r
505   public void ok_actionPerformed(ActionEvent e)\r
506   {\r
507   }\r
508 \r
509   /**\r
510    * DOCUMENT ME!\r
511    *\r
512    * @param e DOCUMENT ME!\r
513    */\r
514   public void cancel_actionPerformed(ActionEvent e)\r
515   {\r
516   }\r
517 \r
518   /**\r
519    * DOCUMENT ME!\r
520    *\r
521    * @param e DOCUMENT ME!\r
522    */\r
523   public void annotations_actionPerformed(ActionEvent e)\r
524   {\r
525   }\r
526 \r
527   /**\r
528    * DOCUMENT ME!\r
529    */\r
530   public void startupFileTextfield_mouseClicked()\r
531   {\r
532   }\r
533 \r
534   public void newLink_actionPerformed(ActionEvent e)\r
535   {\r
536 \r
537   }\r
538 \r
539   public void editLink_actionPerformed(ActionEvent e)\r
540   {\r
541 \r
542   }\r
543 \r
544   public void deleteLink_actionPerformed(ActionEvent e)\r
545   {\r
546 \r
547   }\r
548 \r
549   public void defaultBrowser_mouseClicked(MouseEvent e)\r
550   {\r
551 \r
552   }\r
553 \r
554   public void linkURLList_keyTyped(KeyEvent e)\r
555   {\r
556 \r
557   }\r
558 \r
559   public void useProxy_actionPerformed()\r
560   {\r
561     proxyServerTB.setEnabled(useProxy.isSelected());\r
562     proxyPortTB.setEnabled(useProxy.isSelected());\r
563   }\r
564 \r
565 }\r