2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.jbgui;
22 import java.awt.event.*;
25 import javax.swing.border.*;
26 import javax.swing.event.*;
27 import java.awt.Rectangle;
35 public class GPreferences extends JPanel
37 JTabbedPane tabbedPane = new JTabbedPane();
39 JButton ok = new JButton();
41 JButton cancel = new JButton();
43 JPanel okCancelPanel = new JPanel();
45 BorderLayout borderLayout1 = new BorderLayout();
47 protected JCheckBox quality = new JCheckBox();
49 JPanel visualTab = new JPanel();
51 protected JCheckBox fullScreen = new JCheckBox();
53 protected JCheckBox conservation = new JCheckBox();
55 protected JCheckBox identity = new JCheckBox();
57 protected JCheckBox annotations = new JCheckBox();
59 JLabel gapLabel = new JLabel();
61 protected JComboBox colour = new JComboBox();
63 JLabel colourLabel = new JLabel();
65 JLabel fontLabel = new JLabel();
67 protected JComboBox fontSizeCB = new JComboBox();
69 protected JComboBox fontStyleCB = new JComboBox();
71 protected JComboBox fontNameCB = new JComboBox();
73 protected JComboBox gapSymbolCB = new JComboBox();
75 protected JCheckBox startupCheckbox = new JCheckBox();
77 protected JTextField startupFileTextfield = new JTextField();
79 JPanel connectTab = new JPanel();
81 JLabel serverLabel = new JLabel();
83 protected JList linkURLList = new JList();
85 protected JTextField proxyServerTB = new JTextField();
87 protected JTextField proxyPortTB = new JTextField();
89 JLabel portLabel = new JLabel();
91 JLabel browserLabel = new JLabel();
93 protected JTextField defaultBrowser = new JTextField();
95 JButton newLink = new JButton();
97 JButton editLink = new JButton();
99 JButton deleteLink = new JButton();
101 JScrollPane linkScrollPane = new JScrollPane();
103 JPanel linkPanel = new JPanel();
105 BorderLayout borderLayout2 = new BorderLayout();
107 JPanel editLinkButtons = new JPanel();
109 GridLayout gridLayout1 = new GridLayout();
111 protected JList linkNameList = new JList();
113 JPanel linkPanel2 = new JPanel();
115 BorderLayout borderLayout3 = new BorderLayout();
117 protected JCheckBox useProxy = new JCheckBox();
119 JPanel jPanel1 = new JPanel();
121 TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
123 TitledBorder titledBorder2 = new TitledBorder("File Output");
125 GridBagLayout gridBagLayout2 = new GridBagLayout();
127 GridBagLayout gridBagLayout1 = new GridBagLayout();
129 GridBagLayout gridBagLayout3 = new GridBagLayout();
131 protected JComboBox sortby = new JComboBox();
133 JLabel sortLabel = new JLabel();
135 JPanel jPanel2 = new JPanel();
137 GridLayout gridLayout2 = new GridLayout();
139 JPanel jPanel3 = new JPanel();
141 JPanel autoAnnotSettings1 = new JPanel();
143 JPanel autoAnnotSettings2 = new JPanel();
145 JPanel exportTab = new JPanel();
147 JLabel epsLabel = new JLabel();
149 protected JComboBox epsRendering = new JComboBox();
151 JLabel jLabel1 = new JLabel();
153 protected JCheckBox blcjv = new JCheckBox();
155 protected JCheckBox pileupjv = new JCheckBox();
157 protected JCheckBox clustaljv = new JCheckBox();
159 protected JCheckBox msfjv = new JCheckBox();
161 protected JCheckBox fastajv = new JCheckBox();
163 protected JCheckBox pfamjv = new JCheckBox();
165 FlowLayout flowLayout1 = new FlowLayout();
167 protected JCheckBox pirjv = new JCheckBox();
169 JPanel jPanel11 = new JPanel();
171 Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
173 protected JCheckBox seqLimit = new JCheckBox();
175 GridLayout gridLayout3 = new GridLayout();
177 protected JCheckBox smoothFont = new JCheckBox();
179 JPanel calcTab = new JPanel();
181 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
183 protected JCheckBox padGaps = new JCheckBox();
185 protected JCheckBox modellerOutput = new JCheckBox();
187 protected JPanel dasPanel = new JPanel();
189 BorderLayout borderLayout4 = new BorderLayout();
191 protected JCheckBox wrap = new JCheckBox();
193 protected JCheckBox rightAlign = new JCheckBox();
195 protected JCheckBox showUnconserved = new JCheckBox();
197 protected JCheckBox idItalics = new JCheckBox();
199 protected JCheckBox openoverv = new JCheckBox();
200 protected JCheckBox usagestats = new JCheckBox();
201 protected JCheckBox questionnaire = new JCheckBox();
202 protected JCheckBox versioncheck = new JCheckBox();
203 protected JLabel showGroupbits = new JLabel();
204 protected JLabel showConsensbits = new JLabel();
205 protected JCheckBox showConsensProfile = new JCheckBox();
206 protected JCheckBox showConsensHistogram = new JCheckBox();
207 protected JCheckBox showGroupConsensus = new JCheckBox();
208 protected JCheckBox showGroupConservation = new JCheckBox();
211 * Creates a new GPreferences object.
213 public GPreferences()
218 } catch (Exception ex)
220 ex.printStackTrace();
230 private void jbInit() throws Exception
232 this.setLayout(borderLayout1);
234 ok.addActionListener(new ActionListener()
236 public void actionPerformed(ActionEvent e)
238 ok_actionPerformed(e);
241 cancel.setText("Cancel");
242 cancel.addActionListener(new ActionListener()
244 public void actionPerformed(ActionEvent e)
246 cancel_actionPerformed(e);
249 quality.setEnabled(false);
250 quality.setFont(verdana11);
251 quality.setHorizontalAlignment(SwingConstants.RIGHT);
252 quality.setHorizontalTextPosition(SwingConstants.LEFT);
253 quality.setSelected(true);
254 quality.setText("Quality");
255 visualTab.setBorder(new TitledBorder("Open new alignment"));
256 visualTab.setLayout(null);
257 fullScreen.setFont(verdana11);
258 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
259 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
260 fullScreen.setText("Maximise Window");
261 conservation.setEnabled(false);
262 conservation.setFont(verdana11);
263 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
264 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
265 conservation.setSelected(true);
266 conservation.setText("Conservation");
267 identity.setEnabled(false);
268 identity.setFont(verdana11);
269 identity.setHorizontalAlignment(SwingConstants.RIGHT);
270 identity.setHorizontalTextPosition(SwingConstants.LEFT);
271 identity.setSelected(true);
272 identity.setText("Consensus");
273 showGroupbits.setFont(verdana11);
274 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
275 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
276 showGroupbits.setText("Group:");
277 showConsensbits.setFont(verdana11);
278 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
279 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
280 showConsensbits.setText("Consensus:");
281 showConsensHistogram.setEnabled(false);
282 showConsensHistogram.setFont(verdana11);
283 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
284 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
285 showConsensHistogram.setSelected(true);
286 showConsensHistogram.setText("Histogram");
287 showConsensProfile.setEnabled(false);
288 showConsensProfile.setFont(verdana11);
289 showConsensProfile.setHorizontalAlignment(SwingConstants.RIGHT);
290 showConsensProfile.setHorizontalTextPosition(SwingConstants.LEFT);
291 showConsensProfile.setSelected(true);
292 showConsensProfile.setText("Profile");
293 showGroupConsensus.setEnabled(false);
294 showGroupConsensus.setFont(verdana11);
295 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
296 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
297 showGroupConsensus.setSelected(true);
298 showGroupConsensus.setText("Consensus");
299 showGroupConservation.setEnabled(false);
300 showGroupConservation.setFont(verdana11);
301 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
302 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
303 showGroupConservation.setSelected(true);
304 showGroupConservation.setText("Conservation");
305 annotations.setFont(verdana11);
306 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
307 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
308 annotations.setSelected(true);
309 annotations.setText("Show Annotations");
310 annotations.addActionListener(new ActionListener()
312 public void actionPerformed(ActionEvent e)
314 annotations_actionPerformed(e);
317 showUnconserved.setFont(verdana11);
318 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
319 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
320 //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
321 showUnconserved.setSelected(true);
322 showUnconserved.setText("Show Unconserved");
323 showUnconserved.addActionListener(new ActionListener()
325 public void actionPerformed(ActionEvent e)
327 showunconserved_actionPerformed(e);
331 gapLabel.setFont(verdana11);
332 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
333 gapLabel.setText("Gap Symbol ");
334 colour.setFont(verdana11);
335 colour.setBounds(new Rectangle(172, 225, 155, 21));
336 colourLabel.setFont(verdana11);
337 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
338 colourLabel.setText("Colour ");
339 fontLabel.setFont(verdana11);
340 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
341 fontLabel.setText("Font ");
342 fontSizeCB.setFont(verdana11);
343 fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
344 fontStyleCB.setFont(verdana11);
345 fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
346 fontNameCB.setFont(verdana11);
347 fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
348 gapSymbolCB.setFont(verdana11);
349 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
350 startupCheckbox.setText("Open file");
351 startupCheckbox.setFont(verdana11);
352 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
353 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
354 startupCheckbox.setSelected(true);
355 startupFileTextfield.setFont(verdana11);
356 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
357 startupFileTextfield.addMouseListener(new MouseAdapter()
359 public void mouseClicked(MouseEvent e)
361 if (e.getClickCount() > 1)
363 startupFileTextfield_mouseClicked();
368 connectTab.setLayout(gridBagLayout3);
369 serverLabel.setText("Address");
370 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
371 serverLabel.setFont(verdana11);
372 proxyServerTB.setFont(verdana11);
373 proxyPortTB.setFont(verdana11);
374 portLabel.setFont(verdana11);
375 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
376 portLabel.setText("Port");
377 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
378 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
379 browserLabel.setText("Default Browser (Unix)");
380 defaultBrowser.setFont(verdana11);
381 defaultBrowser.setText("");
382 usagestats.setText("Send usage statistics");
383 usagestats.setFont(verdana11);
384 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
385 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
386 questionnaire.setText("Check for questionnaires");
387 questionnaire.setFont(verdana11);
388 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
389 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
390 versioncheck.setText("Check for latest version");
391 versioncheck.setFont(verdana11);
392 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
393 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
394 newLink.setText("New");
395 newLink.addActionListener(new java.awt.event.ActionListener()
397 public void actionPerformed(ActionEvent e)
399 newLink_actionPerformed(e);
402 editLink.setText("Edit");
403 editLink.addActionListener(new java.awt.event.ActionListener()
405 public void actionPerformed(ActionEvent e)
407 editLink_actionPerformed(e);
410 deleteLink.setText("Delete");
411 deleteLink.addActionListener(new java.awt.event.ActionListener()
413 public void actionPerformed(ActionEvent e)
415 deleteLink_actionPerformed(e);
419 linkURLList.addListSelectionListener(new ListSelectionListener()
421 public void valueChanged(ListSelectionEvent e)
423 int index = linkURLList.getSelectedIndex();
424 linkNameList.setSelectedIndex(index);
428 linkNameList.addListSelectionListener(new ListSelectionListener()
430 public void valueChanged(ListSelectionEvent e)
432 int index = linkNameList.getSelectedIndex();
433 linkURLList.setSelectedIndex(index);
437 linkScrollPane.setBorder(null);
438 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
439 linkPanel.setLayout(borderLayout2);
440 editLinkButtons.setLayout(gridLayout1);
441 gridLayout1.setRows(3);
442 linkNameList.setFont(verdana11);
443 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
444 linkPanel2.setLayout(borderLayout3);
445 linkURLList.setFont(verdana11);
446 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
448 defaultBrowser.addMouseListener(new MouseAdapter()
450 public void mouseClicked(MouseEvent e)
452 if (e.getClickCount() > 1)
454 defaultBrowser_mouseClicked(e);
458 useProxy.setFont(verdana11);
459 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
460 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
461 useProxy.setText("Use a proxy server");
462 useProxy.addActionListener(new ActionListener()
464 public void actionPerformed(ActionEvent e)
466 useProxy_actionPerformed();
469 jPanel1.setBorder(titledBorder1);
470 jPanel1.setLayout(gridBagLayout1);
471 sortby.setFont(verdana11);
472 sortby.setBounds(new Rectangle(172, 249, 155, 21));
473 sortLabel.setFont(verdana11);
474 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
475 sortLabel.setText("Sort by ");
476 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
477 jPanel2.setLayout(gridLayout2);
478 gridLayout2.setRows(13);
479 jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
480 autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
481 autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
482 exportTab.setLayout(null);
483 epsLabel.setFont(verdana11);
484 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
485 epsLabel.setText("EPS Rendering Style");
486 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
487 epsRendering.setFont(verdana11);
488 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
489 jLabel1.setFont(verdana11);
490 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
491 jLabel1.setText("Append /start-end (/15-380)");
492 jLabel1.setFont(verdana11);
493 fastajv.setFont(verdana11);
494 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
495 clustaljv.setText("Clustal ");
496 blcjv.setText("BLC ");
497 fastajv.setText("Fasta ");
498 msfjv.setText("MSF ");
499 pfamjv.setText("PFAM ");
500 pileupjv.setText("Pileup ");
501 msfjv.setFont(verdana11);
502 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
503 pirjv.setText("PIR ");
504 jPanel11.setFont(verdana11);
505 jPanel11.setBorder(titledBorder2);
506 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
507 jPanel11.setLayout(gridLayout3);
508 blcjv.setFont(verdana11);
509 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
510 clustaljv.setFont(verdana11);
511 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
512 pfamjv.setFont(verdana11);
513 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
514 pileupjv.setFont(verdana11);
515 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
516 pirjv.setFont(verdana11);
517 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
518 seqLimit.setFont(verdana11);
519 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
520 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
521 seqLimit.setText("Full Sequence Id");
522 gridLayout3.setRows(8);
523 smoothFont.setFont(verdana11);
524 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
525 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
526 smoothFont.setText("Smooth Font");
527 calcTab.setLayout(null);
528 autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
530 autoCalculateConsCheck.setText("AutoCalculate Consensus");
531 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
532 padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
533 padGaps.setText("Pad gaps when editing");
534 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
535 modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
536 modellerOutput.setText("Use Modeller Output");
537 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
538 dasPanel.setLayout(borderLayout4);
539 wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
540 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
541 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
542 wrap.setText("Wrap Alignment");
543 rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
544 rightAlign.setForeground(Color.black);
545 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
546 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
547 rightAlign.setText("Right Align Ids");
548 idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
549 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
550 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
551 idItalics.setText("Sequence Name Italics");
552 openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
553 openoverv.setActionCommand("Open Overview");
554 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
555 openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
556 openoverv.setText("Open Overview Window");
557 openoverv.setBounds(new Rectangle(169, 17, 200, 23));
558 jPanel2.add(fullScreen);
559 jPanel2.add(annotations);
560 jPanel2.add(seqLimit);
561 jPanel2.add(rightAlign);
562 jPanel2.add(fontLabel);
563 jPanel2.add(showUnconserved);
564 jPanel2.add(idItalics);
565 jPanel2.add(smoothFont);
567 jPanel2.add(gapLabel);
568 jPanel2.add(colourLabel);
569 jPanel2.add(sortLabel);
570 jPanel2.add(startupCheckbox);
571 visualTab.add(openoverv);
572 visualTab.add(startupFileTextfield);
573 visualTab.add(sortby);
574 visualTab.add(colour);
575 visualTab.add(gapSymbolCB);
576 visualTab.add(jPanel3);
577 visualTab.add(fontNameCB);
578 visualTab.add(fontSizeCB);
579 visualTab.add(fontStyleCB);
580 visualTab.add(autoAnnotSettings1);
581 visualTab.add(autoAnnotSettings2);
582 jPanel3.add(conservation);
583 jPanel3.add(identity);
584 jPanel3.add(quality);
585 autoAnnotSettings1.setLayout(new FlowLayout());
586 autoAnnotSettings2.setLayout(new FlowLayout());
587 autoAnnotSettings1.add(showConsensbits);
588 autoAnnotSettings1.add(showConsensHistogram);
589 autoAnnotSettings1.add(showConsensProfile);
590 autoAnnotSettings2.add(showGroupbits);
591 autoAnnotSettings2.add(showGroupConsensus);
592 autoAnnotSettings2.add(showGroupConservation);
593 visualTab.add(jPanel2);
595 linkPanel.add(editLinkButtons, BorderLayout.EAST);
596 editLinkButtons.add(newLink, null);
597 editLinkButtons.add(editLink, null);
598 editLinkButtons.add(deleteLink, null);
599 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
600 linkScrollPane.getViewport().add(linkPanel2, null);
601 linkPanel2.add(linkURLList, BorderLayout.CENTER);
602 linkPanel2.add(linkNameList, BorderLayout.WEST);
603 okCancelPanel.add(ok);
604 okCancelPanel.add(cancel);
605 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
607 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
608 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
609 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
611 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
612 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
614 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
615 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
616 16, 0, 0, 12), 359, -17));
617 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
618 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
619 21, 0, 35, 12), 4, 6));
620 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
621 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
622 new Insets(16, 0, 0, 0), 5, 1));
623 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
624 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
625 new Insets(0, 2, 4, 2), 54, 1));
626 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
627 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
628 new Insets(0, 2, 4, 0), 263, 1));
629 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
630 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
631 new Insets(15, 0, 0, 15), 307, 1));
632 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0,
633 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
634 new Insets(0, 2, 4,2), 70, 1));
635 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
636 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
637 new Insets(0, 2, 4,2), 70, 1));
638 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
639 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
640 new Insets(0, 2, 4,2), 70, 1));
642 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
643 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
645 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
646 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
647 gapSymbolCB.setRenderer(dlcr);
649 tabbedPane.add(visualTab, "Visual");
650 tabbedPane.add(connectTab, "Connections");
651 tabbedPane.add(exportTab, "Output");
652 jPanel11.add(jLabel1);
654 jPanel11.add(clustaljv);
655 jPanel11.add(fastajv);
657 jPanel11.add(pfamjv);
658 jPanel11.add(pileupjv);
660 exportTab.add(modellerOutput);
661 tabbedPane.add(calcTab, "Editing");
662 calcTab.add(autoCalculateConsCheck);
663 calcTab.add(padGaps);
664 tabbedPane.add(dasPanel, "DAS Settings");
666 exportTab.add(epsLabel);
667 exportTab.add(epsRendering);
668 exportTab.add(jPanel11);
671 protected void showunconserved_actionPerformed(ActionEvent e)
673 // TODO Auto-generated method stub
683 public void ok_actionPerformed(ActionEvent e)
693 public void cancel_actionPerformed(ActionEvent e)
703 public void annotations_actionPerformed(ActionEvent e)
710 public void startupFileTextfield_mouseClicked()
714 public void newLink_actionPerformed(ActionEvent e)
719 public void editLink_actionPerformed(ActionEvent e)
724 public void deleteLink_actionPerformed(ActionEvent e)
729 public void defaultBrowser_mouseClicked(MouseEvent e)
734 public void linkURLList_keyTyped(KeyEvent e)
739 public void useProxy_actionPerformed()
741 proxyServerTB.setEnabled(useProxy.isSelected());
742 proxyPortTB.setEnabled(useProxy.isSelected());