Use visible id for sorting
[jalview.git] / src / jalview / jbgui / GPreferences.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 \r
23 import javax.swing.*;\r
24 import javax.swing.border.TitledBorder;\r
25 import java.awt.event.*;\r
26 import javax.swing.event.*;\r
27 \r
28 \r
29 /**\r
30  * DOCUMENT ME!\r
31  *\r
32  * @author $author$\r
33  * @version $Revision$\r
34  */\r
35 public class GPreferences 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 dbRef = new JCheckBox();\r
46     protected JCheckBox fullScreen = new JCheckBox();\r
47     protected JCheckBox conservation = new JCheckBox();\r
48     protected JCheckBox identity = new JCheckBox();\r
49     protected JCheckBox annotations = new JCheckBox();\r
50     JLabel gapLabel = new JLabel();\r
51     protected JComboBox colour = new JComboBox();\r
52     JLabel colourLabel = new JLabel();\r
53     JLabel fontLabel = new JLabel();\r
54     protected JComboBox fontSizeCB = new JComboBox();\r
55     protected JComboBox fontStyleCB = new JComboBox();\r
56     protected JComboBox fontNameCB = new JComboBox();\r
57     protected JComboBox gapSymbolCB = new JComboBox();\r
58     protected JCheckBox startupCheckbox = new JCheckBox();\r
59     protected JTextField startupFileTextfield = new JTextField();\r
60   JPanel connectTab = new JPanel();\r
61   JLabel serverLabel = new JLabel();\r
62   protected JList linkURLList = new JList();\r
63   protected JTextField proxyServerTB = new JTextField();\r
64   protected JTextField proxyPortTB = new JTextField();\r
65   JLabel portLabel = new JLabel();\r
66   JLabel browserLabel = new JLabel();\r
67   protected JTextField defaultBrowser = new JTextField();\r
68   JButton newLink = new JButton();\r
69   JButton editLink = new JButton();\r
70   JButton deleteLink = new JButton();\r
71   JScrollPane linkScrollPane = new JScrollPane();\r
72   JPanel linkPanel = new JPanel();\r
73   BorderLayout borderLayout2 = new BorderLayout();\r
74   JPanel editLinkButtons = new JPanel();\r
75   GridLayout gridLayout1 = new GridLayout();\r
76   protected JList linkNameList = new JList();\r
77   JPanel linkPanel2 = new JPanel();\r
78   BorderLayout borderLayout3 = new BorderLayout();\r
79   protected JCheckBox useProxy = new JCheckBox();\r
80   JPanel jPanel1 = new JPanel();\r
81   TitledBorder titledBorder1 = new TitledBorder("Proxy Server");\r
82   TitledBorder titledBorder2 = new TitledBorder("File Output");\r
83   GridBagLayout gridBagLayout2 = new GridBagLayout();\r
84   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
85   GridBagLayout gridBagLayout3 = new GridBagLayout();\r
86   protected JComboBox sortby = new JComboBox();\r
87   JLabel sortLabel = new JLabel();\r
88   JPanel jPanel2 = new JPanel();\r
89   GridLayout gridLayout2 = new GridLayout();\r
90   JPanel jPanel3 = new JPanel();\r
91   JPanel exportTab = new JPanel();\r
92   JLabel epsLabel = new JLabel();\r
93   protected JComboBox epsRendering = new JComboBox();\r
94   JLabel jLabel1 = new JLabel();\r
95   JLabel jLabel2 = new JLabel();\r
96   protected JCheckBox pileupdb = new JCheckBox();\r
97   protected  JCheckBox fastadb = new JCheckBox();\r
98   protected  JCheckBox blcjv = new JCheckBox();\r
99   protected  JCheckBox pileupjv = new JCheckBox();\r
100   protected  JCheckBox msfdb = new JCheckBox();\r
101   protected  JCheckBox pfamdb = new JCheckBox();\r
102   protected  JCheckBox clustaljv = new JCheckBox();\r
103   protected  JCheckBox msfjv = new JCheckBox();\r
104   protected  JCheckBox blcdb = new JCheckBox();\r
105   protected  JCheckBox clustaldb = new JCheckBox();\r
106   protected  JCheckBox fastajv = new JCheckBox();\r
107   protected  JCheckBox pfamjv = new JCheckBox();\r
108   JLabel jLabel10 = new JLabel();\r
109   JLabel jLabel11 = new JLabel();\r
110   FlowLayout flowLayout1 = new FlowLayout();\r
111   protected  JCheckBox pirdb = new JCheckBox();\r
112   protected  JCheckBox pirjv = new JCheckBox();\r
113   JPanel jPanel11 = new JPanel();\r
114   GridLayout gridLayout3 = new GridLayout();\r
115   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
116   protected JCheckBox seqLimit = 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() throws Exception\r
138     {\r
139         this.setLayout(borderLayout1);\r
140         ok.setText("OK");\r
141         ok.addActionListener(new ActionListener()\r
142             {\r
143                 public void actionPerformed(ActionEvent e)\r
144                 {\r
145                     ok_actionPerformed(e);\r
146                 }\r
147             });\r
148         cancel.setText("Cancel");\r
149         cancel.addActionListener(new ActionListener()\r
150             {\r
151                 public void actionPerformed(ActionEvent e)\r
152                 {\r
153                     cancel_actionPerformed(e);\r
154                 }\r
155             });\r
156         quality.setEnabled(false);\r
157         quality.setFont(verdana11);\r
158         quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
159         quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
160         quality.setSelected(true);\r
161         quality.setText("Quality");\r
162     visualTab.setBorder(new TitledBorder("Open new alignment"));\r
163     visualTab.setLayout(null);\r
164     dbRef.setFont(verdana11);\r
165     dbRef.setHorizontalAlignment(SwingConstants.RIGHT);\r
166     dbRef.setHorizontalTextPosition(SwingConstants.LEFT);\r
167     dbRef.setMargin(new Insets(4, 2, 2, 0));\r
168     dbRef.setText("DB prefix (DB|AccNo)");\r
169     fullScreen.setFont(verdana11);\r
170         fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
171         fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
172     fullScreen.setMargin(new Insets(2, 2, 2, 0));\r
173     fullScreen.setText("Maximise Window");\r
174     conservation.setEnabled(false);\r
175         conservation.setFont(verdana11);\r
176         conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
177         conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
178         conservation.setSelected(true);\r
179         conservation.setText("Conservation");\r
180     identity.setEnabled(false);\r
181         identity.setFont(verdana11);\r
182         identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
183         identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
184         identity.setSelected(true);\r
185         identity.setText("Consensus");\r
186     annotations.setFont(verdana11);\r
187         annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
188         annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
189     annotations.setMargin(new Insets(2, 4, 2, 0));\r
190     annotations.setSelected(true);\r
191         annotations.setText("Show Annotations");\r
192     annotations.addActionListener(new ActionListener()\r
193             {\r
194                 public void actionPerformed(ActionEvent e)\r
195                 {\r
196                     annotations_actionPerformed(e);\r
197                 }\r
198             });\r
199         gapLabel.setFont(verdana11);\r
200         gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
201         gapLabel.setText("Gap Symbol ");\r
202     colour.setFont(verdana11);\r
203         colour.setBounds(new Rectangle(170, 170, 155, 21));\r
204         colourLabel.setFont(verdana11);\r
205         colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
206         colourLabel.setText("Colour ");\r
207     fontLabel.setFont(verdana11);\r
208         fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
209         fontLabel.setText("Font ");\r
210     fontSizeCB.setFont(verdana11);\r
211         fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));\r
212         fontStyleCB.setFont(verdana11);\r
213         fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));\r
214         fontNameCB.setFont(verdana11);\r
215         fontNameCB.setBounds(new Rectangle(170, 111, 147, 21));\r
216         gapSymbolCB.setFont(verdana11);\r
217         gapSymbolCB.setBounds(new Rectangle(170, 141, 69, 21));\r
218         startupCheckbox.setText("Open file");\r
219     startupCheckbox.setFont(verdana11);\r
220         startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
221         startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
222         startupCheckbox.setSelected(true);\r
223         startupFileTextfield.setFont(verdana11);\r
224         startupFileTextfield.setBounds(new Rectangle(170, 232, 271, 20));\r
225         startupFileTextfield.addMouseListener(new MouseAdapter()\r
226             {\r
227                 public void mouseClicked(MouseEvent e)\r
228                 {\r
229                     if (e.getClickCount() > 1)\r
230                     {\r
231                         startupFileTextfield_mouseClicked();\r
232                     }\r
233                 }\r
234             });\r
235 \r
236      connectTab.setLayout(gridBagLayout3);\r
237     serverLabel.setText("Address");\r
238     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
239     serverLabel.setFont(verdana11);\r
240     proxyServerTB.setFont(verdana11);\r
241     proxyPortTB.setFont(verdana11);\r
242     portLabel.setFont(verdana11);\r
243     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
244     portLabel.setText("Port");\r
245     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));\r
246     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);\r
247     browserLabel.setText("Default Browser (Unix)");\r
248     defaultBrowser.setFont(verdana11);\r
249     defaultBrowser.setText("");\r
250     newLink.setText("New");\r
251     newLink.addActionListener(new java.awt.event.ActionListener() {\r
252       public void actionPerformed(ActionEvent e) {\r
253         newLink_actionPerformed(e);\r
254       }\r
255     });\r
256     editLink.setText("Edit");\r
257     editLink.addActionListener(new java.awt.event.ActionListener() {\r
258       public void actionPerformed(ActionEvent e) {\r
259         editLink_actionPerformed(e);\r
260       }\r
261     });\r
262     deleteLink.setText("Delete");\r
263     deleteLink.addActionListener(new java.awt.event.ActionListener() {\r
264       public void actionPerformed(ActionEvent e) {\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(new java.awt.Font("Verdana", Font.ITALIC, 11));\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(170, 200, 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, 242));\r
327     jPanel2.setLayout(gridLayout2);\r
328     gridLayout2.setRows(8);\r
329     jPanel3.setBounds(new Rectangle(168, 47, 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("/start-end suffix");\r
340     jLabel2.setFont(verdana11);\r
341     jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
342     jLabel2.setHorizontalTextPosition(SwingConstants.RIGHT);\r
343     jLabel2.setText("Database ref prefix");\r
344     jLabel1.setFont(verdana11);\r
345     jLabel2.setFont(verdana11);\r
346     fastajv.setFont(verdana11);\r
347     fastajv.setHorizontalAlignment(SwingConstants.CENTER);\r
348     jLabel10.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
349     jLabel10.setHorizontalAlignment(SwingConstants.RIGHT);\r
350     jLabel10.setText("(Uniprot|P02055)");\r
351     jLabel11.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
352     jLabel11.setHorizontalAlignment(SwingConstants.CENTER);\r
353     jLabel11.setText("(/15-380)");\r
354     clustaldb.setFont(verdana11);\r
355     clustaldb.setHorizontalAlignment(SwingConstants.RIGHT);\r
356     clustaldb.setHorizontalTextPosition(SwingConstants.LEFT);\r
357     clustaldb.setText("Clustal     ");\r
358     blcdb.setFont(verdana11);\r
359     blcdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
360     blcdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
361     blcdb.setText("BLC     ");\r
362     fastadb.setFont(verdana11);\r
363     fastadb.setHorizontalAlignment(SwingConstants.RIGHT);\r
364     fastadb.setHorizontalTextPosition(SwingConstants.LEFT);\r
365     fastadb.setText("Fasta     ");\r
366     msfdb.setFont(verdana11);\r
367     msfdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
368     msfdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
369     msfdb.setText("MSF     ");\r
370     pfamdb.setFont(verdana11);\r
371     pfamdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
372     pfamdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
373     pfamdb.setText("PFAM     ");\r
374     pileupdb.setFont(verdana11);\r
375     pileupdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
376     pileupdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
377     pileupdb.setText("Pileup     ");\r
378     msfjv.setFont(verdana11);\r
379     msfjv.setHorizontalAlignment(SwingConstants.CENTER);\r
380     pirdb.setFont(verdana11);\r
381     pirdb.setHorizontalAlignment(SwingConstants.RIGHT);\r
382     pirdb.setHorizontalTextPosition(SwingConstants.LEFT);\r
383     pirdb.setText("PIR     ");\r
384     jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
385     jPanel11.setBorder(titledBorder2);\r
386     jPanel11.setBounds(new Rectangle(18, 72, 325, 182));\r
387     jPanel11.setLayout(gridLayout3);\r
388     gridLayout3.setColumns(2);\r
389     gridLayout3.setRows(9);\r
390     blcjv.setFont(verdana11);\r
391     blcjv.setHorizontalAlignment(SwingConstants.CENTER);\r
392     clustaljv.setFont(verdana11);\r
393     clustaljv.setHorizontalAlignment(SwingConstants.CENTER);\r
394     pfamjv.setFont(verdana11);\r
395     pfamjv.setHorizontalAlignment(SwingConstants.CENTER);\r
396     pileupjv.setFont(verdana11);\r
397     pileupjv.setHorizontalAlignment(SwingConstants.CENTER);\r
398     pirjv.setFont(verdana11);\r
399     pirjv.setHorizontalAlignment(SwingConstants.CENTER);\r
400     seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
401     seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);\r
402     seqLimit.setText("Sequence Limits (/1-350)");\r
403     seqLimit.setBounds(new Rectangle(172, 82, 195, 23));\r
404     jPanel2.add(fullScreen);\r
405     jPanel2.add(annotations);\r
406     jPanel2.add(dbRef);\r
407     jPanel2.add(fontLabel);\r
408     jPanel2.add(gapLabel);\r
409     jPanel2.add(colourLabel);\r
410     jPanel2.add(sortLabel);\r
411     jPanel2.add(startupCheckbox);\r
412     visualTab.add(gapSymbolCB);\r
413     visualTab.add(colour);\r
414     visualTab.add(seqLimit);\r
415     visualTab.add(jPanel3);\r
416     jPanel3.add(conservation);\r
417     jPanel3.add(identity);\r
418     jPanel3.add(quality);\r
419     visualTab.add(sortby);\r
420     visualTab.add(startupFileTextfield);\r
421     visualTab.add(fontNameCB);\r
422     visualTab.add(fontSizeCB);\r
423     visualTab.add(fontStyleCB);\r
424     visualTab.add(jPanel2);\r
425     linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
426     editLinkButtons.add(newLink, null);\r
427     editLinkButtons.add(editLink, null);\r
428     editLinkButtons.add(deleteLink, null);\r
429     linkPanel.add(linkScrollPane, BorderLayout.CENTER);\r
430     linkScrollPane.getViewport().add(linkPanel2, null);\r
431     linkPanel2.add(linkURLList, BorderLayout.CENTER);\r
432     linkPanel2.add(linkNameList, BorderLayout.WEST);\r
433         okCancelPanel.add(ok);\r
434         okCancelPanel.add(cancel);\r
435     this.add(tabbedPane, java.awt.BorderLayout.CENTER);\r
436 \r
437         this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);\r
438     jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
439         , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
440         new Insets(0, 2, 4, 0), 5, 0));\r
441     jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0\r
442                                                   , GridBagConstraints.WEST,\r
443                                                   GridBagConstraints.NONE,\r
444                                                   new Insets(0, 0, 4, 0), 11, 6));\r
445     connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0\r
446         , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
447         new Insets(16, 0, 0, 12), 359, -17));\r
448     connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
449         , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
450         new Insets(21, 0, 35, 12), 4, 6));\r
451     connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
452         , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
453         new Insets(16, 0, 0, 0), 5, 1));\r
454     jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0\r
455         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
456         new Insets(0, 2, 4, 2), 54, 1));\r
457     jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
458         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
459         new Insets(0, 2, 4, 0), 263, 1));\r
460     connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
461         , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
462         new Insets(15, 0, 0, 15), 307, 1));\r
463 \r
464 \r
465     jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
466                                                  , GridBagConstraints.WEST,\r
467                                                  GridBagConstraints.NONE,\r
468                                                  new Insets(0, 2, 5, 185), 2,\r
469                                                  -4));\r
470     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();\r
471         dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
472         gapSymbolCB.setRenderer(dlcr);\r
473 \r
474     tabbedPane.add(visualTab, "Visual");\r
475     tabbedPane.add(connectTab,"Connections");\r
476     tabbedPane.add(exportTab, "Output");\r
477     jPanel11.add(jLabel2);\r
478     jPanel11.add(jLabel1);\r
479     jPanel11.add(jLabel10);\r
480     jPanel11.add(jLabel11);\r
481     jPanel11.add(blcdb);\r
482     jPanel11.add(blcjv);\r
483     jPanel11.add(clustaldb);\r
484     jPanel11.add(clustaljv);\r
485     jPanel11.add(fastadb);\r
486     jPanel11.add(fastajv);\r
487     jPanel11.add(msfdb);\r
488     jPanel11.add(msfjv);\r
489     jPanel11.add(pfamdb);\r
490     jPanel11.add(pfamjv);\r
491     jPanel11.add(pileupdb);\r
492     jPanel11.add(pileupjv);\r
493     jPanel11.add(pirdb);\r
494     jPanel11.add(pirjv);\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     /**\r
529      * DOCUMENT ME!\r
530      */\r
531     public void startupFileTextfield_mouseClicked()\r
532     {\r
533     }\r
534 \r
535 \r
536   public void newLink_actionPerformed(ActionEvent e) {\r
537 \r
538   }\r
539 \r
540   public void editLink_actionPerformed(ActionEvent e) {\r
541 \r
542   }\r
543 \r
544   public void deleteLink_actionPerformed(ActionEvent e) {\r
545 \r
546   }\r
547 \r
548   public void defaultBrowser_mouseClicked(MouseEvent e)\r
549   {\r
550 \r
551   }\r
552 \r
553   public void linkURLList_keyTyped(KeyEvent e)\r
554   {\r
555 \r
556   }\r
557 \r
558   public void useProxy_actionPerformed()\r
559   {\r
560       proxyServerTB.setEnabled(useProxy.isSelected());\r
561       proxyPortTB.setEnabled(useProxy.isSelected());\r
562   }\r
563 }\r