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();
140 JPanel annsettingsPanel = new JPanel();
141 JPanel autoAnnotSettings1 = new JPanel();
142 JPanel autoAnnotSettings2 = new JPanel();
143 JPanel autoAnnotSettings3 = 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 showConsensLogo = new JCheckBox();
206 protected JCheckBox showConsensHistogram = new JCheckBox();
207 protected JCheckBox showGroupConsensus = new JCheckBox();
208 protected JCheckBox showGroupConservation = new JCheckBox();
209 protected JCheckBox shareSelections = new JCheckBox();
210 protected JCheckBox followHighlight = new JCheckBox();
214 * Creates a new GPreferences object.
216 public GPreferences()
221 } catch (Exception ex)
223 ex.printStackTrace();
233 private void jbInit() throws Exception
235 this.setLayout(borderLayout1);
237 ok.addActionListener(new ActionListener()
239 public void actionPerformed(ActionEvent e)
241 ok_actionPerformed(e);
244 cancel.setText("Cancel");
245 cancel.addActionListener(new ActionListener()
247 public void actionPerformed(ActionEvent e)
249 cancel_actionPerformed(e);
252 quality.setEnabled(false);
253 quality.setFont(verdana11);
254 quality.setHorizontalAlignment(SwingConstants.RIGHT);
255 quality.setHorizontalTextPosition(SwingConstants.LEFT);
256 quality.setSelected(true);
257 quality.setText("Quality");
258 visualTab.setBorder(new TitledBorder("Open new alignment"));
259 visualTab.setLayout(null);
260 fullScreen.setFont(verdana11);
261 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
262 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
263 fullScreen.setText("Maximise Window");
264 conservation.setEnabled(false);
265 conservation.setFont(verdana11);
266 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
267 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
268 conservation.setSelected(true);
269 conservation.setText("Conservation");
270 identity.setEnabled(false);
271 identity.setFont(verdana11);
272 identity.setHorizontalAlignment(SwingConstants.RIGHT);
273 identity.setHorizontalTextPosition(SwingConstants.LEFT);
274 identity.setSelected(true);
275 identity.setText("Consensus");
276 showGroupbits.setFont(verdana11);
277 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
278 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
279 showGroupbits.setText("Show group:");
280 showConsensbits.setFont(verdana11);
281 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
282 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
283 showConsensbits.setText("Consensus:");
284 showConsensHistogram.setEnabled(false);
285 showConsensHistogram.setFont(verdana11);
286 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
287 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
288 showConsensHistogram.setSelected(true);
289 showConsensHistogram.setText("Histogram");
290 showConsensLogo.setEnabled(false);
291 showConsensLogo.setFont(verdana11);
292 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
293 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
294 showConsensLogo.setSelected(true);
295 showConsensLogo.setText("Logo");
296 showGroupConsensus.setEnabled(false);
297 showGroupConsensus.setFont(verdana11);
298 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
299 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
300 showGroupConsensus.setSelected(true);
301 showGroupConsensus.setText("Consensus");
302 showGroupConservation.setEnabled(false);
303 showGroupConservation.setFont(verdana11);
304 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
305 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
306 showGroupConservation.setSelected(true);
307 showGroupConservation.setText("Conservation");
308 annotations.setFont(verdana11);
309 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
310 annotations.setHorizontalTextPosition(SwingConstants.LEADING);
311 annotations.setSelected(true);
312 annotations.setText("Show Annotations");
313 annotations.setBounds(new Rectangle(169, 16, 200, 23));
314 annotations.addActionListener(new ActionListener()
316 public void actionPerformed(ActionEvent e)
318 annotations_actionPerformed(e);
321 identity.addActionListener(new ActionListener()
323 public void actionPerformed(ActionEvent e)
325 annotations_actionPerformed(e);
328 showGroupConsensus.addActionListener(new ActionListener()
330 public void actionPerformed(ActionEvent e)
332 annotations_actionPerformed(e);
335 showUnconserved.setFont(verdana11);
336 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
337 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
338 //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
339 showUnconserved.setSelected(true);
340 showUnconserved.setText("Show Unconserved");
341 showUnconserved.addActionListener(new ActionListener()
343 public void actionPerformed(ActionEvent e)
345 showunconserved_actionPerformed(e);
348 shareSelections.setFont(verdana11);
349 shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
350 shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
351 //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
352 shareSelections.setSelected(true);
353 shareSelections.setText("Share selection across views");
354 followHighlight.setFont(verdana11);
355 followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
356 followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
357 //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
358 followHighlight.setSelected(true);
359 followHighlight.setText("Scroll to highlighted regions");
361 gapLabel.setFont(verdana11);
362 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
363 gapLabel.setText("Gap Symbol ");
364 colour.setFont(verdana11);
365 colour.setBounds(new Rectangle(172, 225, 155, 21));
366 colourLabel.setFont(verdana11);
367 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
368 colourLabel.setText("Colour ");
369 fontLabel.setFont(verdana11);
370 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
371 fontLabel.setText("Font ");
372 fontSizeCB.setFont(verdana11);
373 fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
374 fontStyleCB.setFont(verdana11);
375 fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
376 fontNameCB.setFont(verdana11);
377 fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
378 gapSymbolCB.setFont(verdana11);
379 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
380 startupCheckbox.setText("Open file");
381 startupCheckbox.setFont(verdana11);
382 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
383 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
384 startupCheckbox.setSelected(true);
385 startupFileTextfield.setFont(verdana11);
386 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
387 startupFileTextfield.addMouseListener(new MouseAdapter()
389 public void mouseClicked(MouseEvent e)
391 if (e.getClickCount() > 1)
393 startupFileTextfield_mouseClicked();
398 connectTab.setLayout(gridBagLayout3);
399 serverLabel.setText("Address");
400 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
401 serverLabel.setFont(verdana11);
402 proxyServerTB.setFont(verdana11);
403 proxyPortTB.setFont(verdana11);
404 portLabel.setFont(verdana11);
405 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
406 portLabel.setText("Port");
407 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
408 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
409 browserLabel.setText("Default Browser (Unix)");
410 defaultBrowser.setFont(verdana11);
411 defaultBrowser.setText("");
412 usagestats.setText("Send usage statistics");
413 usagestats.setFont(verdana11);
414 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
415 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
416 questionnaire.setText("Check for questionnaires");
417 questionnaire.setFont(verdana11);
418 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
419 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
420 versioncheck.setText("Check for latest version");
421 versioncheck.setFont(verdana11);
422 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
423 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
424 newLink.setText("New");
425 newLink.addActionListener(new java.awt.event.ActionListener()
427 public void actionPerformed(ActionEvent e)
429 newLink_actionPerformed(e);
432 editLink.setText("Edit");
433 editLink.addActionListener(new java.awt.event.ActionListener()
435 public void actionPerformed(ActionEvent e)
437 editLink_actionPerformed(e);
440 deleteLink.setText("Delete");
441 deleteLink.addActionListener(new java.awt.event.ActionListener()
443 public void actionPerformed(ActionEvent e)
445 deleteLink_actionPerformed(e);
449 linkURLList.addListSelectionListener(new ListSelectionListener()
451 public void valueChanged(ListSelectionEvent e)
453 int index = linkURLList.getSelectedIndex();
454 linkNameList.setSelectedIndex(index);
458 linkNameList.addListSelectionListener(new ListSelectionListener()
460 public void valueChanged(ListSelectionEvent e)
462 int index = linkNameList.getSelectedIndex();
463 linkURLList.setSelectedIndex(index);
467 linkScrollPane.setBorder(null);
468 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
469 linkPanel.setLayout(borderLayout2);
470 editLinkButtons.setLayout(gridLayout1);
471 gridLayout1.setRows(3);
472 linkNameList.setFont(verdana11);
473 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
474 linkPanel2.setLayout(borderLayout3);
475 linkURLList.setFont(verdana11);
476 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
478 defaultBrowser.addMouseListener(new MouseAdapter()
480 public void mouseClicked(MouseEvent e)
482 if (e.getClickCount() > 1)
484 defaultBrowser_mouseClicked(e);
488 useProxy.setFont(verdana11);
489 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
490 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
491 useProxy.setText("Use a proxy server");
492 useProxy.addActionListener(new ActionListener()
494 public void actionPerformed(ActionEvent e)
496 useProxy_actionPerformed();
499 jPanel1.setBorder(titledBorder1);
500 jPanel1.setLayout(gridBagLayout1);
501 sortby.setFont(verdana11);
502 sortby.setBounds(new Rectangle(172, 249, 155, 21));
503 sortLabel.setFont(verdana11);
504 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
505 sortLabel.setText("Sort by ");
506 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
507 jPanel2.setLayout(gridLayout2);
508 gridLayout2.setRows(13);
509 // jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
510 //jPanel3.setBounds(new Rectangle(173, 35, 274, 78));
511 //jPanel3.setLayout(new GridLayout(3,3));
512 // autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
513 // autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
514 exportTab.setLayout(null);
515 epsLabel.setFont(verdana11);
516 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
517 epsLabel.setText("EPS Rendering Style");
518 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
519 epsRendering.setFont(verdana11);
520 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
521 jLabel1.setFont(verdana11);
522 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
523 jLabel1.setText("Append /start-end (/15-380)");
524 jLabel1.setFont(verdana11);
525 fastajv.setFont(verdana11);
526 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
527 clustaljv.setText("Clustal ");
528 blcjv.setText("BLC ");
529 fastajv.setText("Fasta ");
530 msfjv.setText("MSF ");
531 pfamjv.setText("PFAM ");
532 pileupjv.setText("Pileup ");
533 msfjv.setFont(verdana11);
534 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
535 pirjv.setText("PIR ");
536 jPanel11.setFont(verdana11);
537 jPanel11.setBorder(titledBorder2);
538 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
539 jPanel11.setLayout(gridLayout3);
540 blcjv.setFont(verdana11);
541 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
542 clustaljv.setFont(verdana11);
543 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
544 pfamjv.setFont(verdana11);
545 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
546 pileupjv.setFont(verdana11);
547 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
548 pirjv.setFont(verdana11);
549 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
550 seqLimit.setFont(verdana11);
551 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
552 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
553 seqLimit.setText("Full Sequence Id");
554 gridLayout3.setRows(8);
555 smoothFont.setFont(verdana11);
556 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
557 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
558 smoothFont.setText("Smooth Font");
559 calcTab.setLayout(null);
560 autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
562 autoCalculateConsCheck.setText("AutoCalculate Consensus");
563 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
564 padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
565 padGaps.setText("Pad gaps when editing");
566 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
567 modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
568 modellerOutput.setText("Use Modeller Output");
569 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
570 dasPanel.setLayout(borderLayout4);
571 wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
572 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
573 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
574 wrap.setText("Wrap Alignment");
575 rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
576 rightAlign.setForeground(Color.black);
577 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
578 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
579 rightAlign.setText("Right Align Ids");
580 idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
581 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
582 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
583 idItalics.setText("Sequence Name Italics");
584 openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
585 openoverv.setActionCommand("Open Overview");
586 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
587 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
588 openoverv.setText("Open Overview");
589 jPanel2.add(fullScreen);
590 jPanel2.add(openoverv);
591 jPanel2.add(seqLimit);
592 jPanel2.add(rightAlign);
593 jPanel2.add(fontLabel);
594 jPanel2.add(showUnconserved);
595 jPanel2.add(idItalics);
596 jPanel2.add(smoothFont);
598 jPanel2.add(gapLabel);
599 jPanel2.add(colourLabel);
600 jPanel2.add(sortLabel);
601 jPanel2.add(startupCheckbox);
602 visualTab.add(annotations);
603 visualTab.add(startupFileTextfield);
604 visualTab.add(sortby);
605 visualTab.add(colour);
606 visualTab.add(gapSymbolCB);
607 visualTab.add(fontNameCB);
608 visualTab.add(fontSizeCB);
609 visualTab.add(fontStyleCB);
610 annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
611 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
612 annsettingsPanel.add(autoAnnotSettings1);
613 annsettingsPanel.add(autoAnnotSettings2);
614 annsettingsPanel.add(autoAnnotSettings3);
615 autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
616 // autoAnnotSettings1.setPreferredSize(new Dimensions())
617 autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
618 autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
619 visualTab.add(annsettingsPanel);
620 //visualTab.add(autoAnnotSettings1);
621 //visualTab.add(autoAnnotSettings2);
622 Border jb = new EmptyBorder(1,1,4,5);
623 quality.setBorder(jb);
624 conservation.setBorder(jb);
625 identity.setBorder(jb);
626 showConsensbits.setBorder(jb);
627 showGroupbits.setBorder(jb);
628 showGroupConsensus.setBorder(jb);
629 showGroupConservation.setBorder(jb);
630 showConsensHistogram.setBorder(jb);
631 showConsensLogo.setBorder(jb);
633 autoAnnotSettings2.add(conservation);
634 autoAnnotSettings1.add(quality);
635 autoAnnotSettings3.add(identity);
637 /*FlowLayout fl = new FlowLayout();
638 fl.setAlignment(FlowLayout.LEFT);
639 autoAnnotSettings1.setLayout(fl);
640 fl = new FlowLayout();
641 fl.setAlignment(FlowLayout.LEFT);
642 autoAnnotSettings2.setLayout(fl); */
643 autoAnnotSettings1.add(showGroupbits);
644 autoAnnotSettings3.add(showGroupConsensus);
645 autoAnnotSettings2.add(showGroupConservation);
646 autoAnnotSettings1.add(showConsensbits);
647 autoAnnotSettings2.add(showConsensHistogram);
648 autoAnnotSettings3.add(showConsensLogo);
649 visualTab.add(jPanel2);
651 linkPanel.add(editLinkButtons, BorderLayout.EAST);
652 editLinkButtons.add(newLink, null);
653 editLinkButtons.add(editLink, null);
654 editLinkButtons.add(deleteLink, null);
655 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
656 linkScrollPane.getViewport().add(linkPanel2, null);
657 linkPanel2.add(linkURLList, BorderLayout.CENTER);
658 linkPanel2.add(linkNameList, BorderLayout.WEST);
659 okCancelPanel.add(ok);
660 okCancelPanel.add(cancel);
661 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
663 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
664 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
665 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
667 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
668 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
670 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
671 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
672 16, 0, 0, 12), 359, -17));
673 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
674 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
675 21, 0, 35, 12), 4, 6));
676 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
677 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
678 new Insets(16, 0, 0, 0), 5, 1));
679 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
680 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
681 new Insets(0, 2, 4, 2), 54, 1));
682 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
683 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
684 new Insets(0, 2, 4, 0), 263, 1));
685 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
686 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
687 new Insets(15, 0, 0, 15), 307, 1));
688 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0,
689 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
690 new Insets(0, 2, 4,2), 70, 1));
691 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
692 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
693 new Insets(0, 2, 4,2), 70, 1));
694 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
695 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
696 new Insets(0, 2, 4,2), 70, 1));
698 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
699 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
701 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
702 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
703 gapSymbolCB.setRenderer(dlcr);
705 tabbedPane.add(visualTab, "Visual");
706 tabbedPane.add(connectTab, "Connections");
707 tabbedPane.add(exportTab, "Output");
708 jPanel11.add(jLabel1);
710 jPanel11.add(clustaljv);
711 jPanel11.add(fastajv);
713 jPanel11.add(pfamjv);
714 jPanel11.add(pileupjv);
716 exportTab.add(modellerOutput);
717 tabbedPane.add(calcTab, "Editing");
718 calcTab.add(autoCalculateConsCheck);
719 calcTab.add(padGaps);
720 tabbedPane.add(dasPanel, "DAS Settings");
722 exportTab.add(epsLabel);
723 exportTab.add(epsRendering);
724 exportTab.add(jPanel11);
727 protected void showunconserved_actionPerformed(ActionEvent e)
729 // TODO Auto-generated method stub
739 public void ok_actionPerformed(ActionEvent e)
749 public void cancel_actionPerformed(ActionEvent e)
759 public void annotations_actionPerformed(ActionEvent e)
766 public void startupFileTextfield_mouseClicked()
770 public void newLink_actionPerformed(ActionEvent e)
775 public void editLink_actionPerformed(ActionEvent e)
780 public void deleteLink_actionPerformed(ActionEvent e)
785 public void defaultBrowser_mouseClicked(MouseEvent e)
790 public void linkURLList_keyTyped(KeyEvent e)
795 public void useProxy_actionPerformed()
797 proxyServerTB.setEnabled(useProxy.isSelected());
798 proxyPortTB.setEnabled(useProxy.isSelected());