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();
196 protected JCheckBox showDbRefTooltip = new JCheckBox();
197 protected JCheckBox showNpTooltip = new JCheckBox();
199 protected JCheckBox idItalics = new JCheckBox();
201 protected JCheckBox openoverv = new JCheckBox();
202 protected JCheckBox usagestats = new JCheckBox();
203 protected JCheckBox questionnaire = new JCheckBox();
204 protected JCheckBox versioncheck = new JCheckBox();
205 protected JLabel showGroupbits = new JLabel();
206 protected JLabel showConsensbits = new JLabel();
207 protected JCheckBox showConsensLogo = new JCheckBox();
208 protected JCheckBox showConsensHistogram = new JCheckBox();
209 protected JCheckBox showGroupConsensus = new JCheckBox();
210 protected JCheckBox showGroupConservation = new JCheckBox();
211 protected JCheckBox shareSelections = new JCheckBox();
212 protected JCheckBox followHighlight = new JCheckBox();
216 * Creates a new GPreferences object.
218 public GPreferences()
223 } catch (Exception ex)
225 ex.printStackTrace();
235 private void jbInit() throws Exception
237 this.setLayout(borderLayout1);
239 ok.addActionListener(new ActionListener()
241 public void actionPerformed(ActionEvent e)
243 ok_actionPerformed(e);
246 cancel.setText("Cancel");
247 cancel.addActionListener(new ActionListener()
249 public void actionPerformed(ActionEvent e)
251 cancel_actionPerformed(e);
254 quality.setEnabled(false);
255 quality.setFont(verdana11);
256 quality.setHorizontalAlignment(SwingConstants.RIGHT);
257 quality.setHorizontalTextPosition(SwingConstants.LEFT);
258 quality.setSelected(true);
259 quality.setText("Quality");
260 visualTab.setBorder(new TitledBorder("Open new alignment"));
261 visualTab.setLayout(null);
262 fullScreen.setFont(verdana11);
263 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
264 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
265 fullScreen.setText("Maximise Window");
266 conservation.setEnabled(false);
267 conservation.setFont(verdana11);
268 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
269 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
270 conservation.setSelected(true);
271 conservation.setText("Conservation");
272 identity.setEnabled(false);
273 identity.setFont(verdana11);
274 identity.setHorizontalAlignment(SwingConstants.RIGHT);
275 identity.setHorizontalTextPosition(SwingConstants.LEFT);
276 identity.setSelected(true);
277 identity.setText("Consensus");
278 showGroupbits.setFont(verdana11);
279 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
280 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
281 showGroupbits.setText("Show group:");
282 showConsensbits.setFont(verdana11);
283 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
284 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
285 showConsensbits.setText("Consensus:");
286 showConsensHistogram.setEnabled(false);
287 showConsensHistogram.setFont(verdana11);
288 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
289 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
290 showConsensHistogram.setSelected(true);
291 showConsensHistogram.setText("Histogram");
292 showConsensLogo.setEnabled(false);
293 showConsensLogo.setFont(verdana11);
294 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
295 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
296 showConsensLogo.setSelected(true);
297 showConsensLogo.setText("Logo");
298 showGroupConsensus.setEnabled(false);
299 showGroupConsensus.setFont(verdana11);
300 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
301 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
302 showGroupConsensus.setSelected(true);
303 showGroupConsensus.setText("Consensus");
304 showGroupConservation.setEnabled(false);
305 showGroupConservation.setFont(verdana11);
306 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
307 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
308 showGroupConservation.setSelected(true);
309 showGroupConservation.setText("Conservation");
310 showNpTooltip.setEnabled(true);
311 showNpTooltip.setFont(verdana11);
312 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
313 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
314 showNpTooltip.setSelected(true);
315 showNpTooltip.setText("Non-positional Features");
316 showDbRefTooltip.setEnabled(true);
317 showDbRefTooltip.setFont(verdana11);
318 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
319 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
320 showDbRefTooltip.setSelected(true);
321 showDbRefTooltip.setText("Database References");
322 annotations.setFont(verdana11);
323 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
324 annotations.setHorizontalTextPosition(SwingConstants.LEADING);
325 annotations.setSelected(true);
326 annotations.setText("Show Annotations");
327 annotations.setBounds(new Rectangle(169, 16, 200, 23));
328 annotations.addActionListener(new ActionListener()
330 public void actionPerformed(ActionEvent e)
332 annotations_actionPerformed(e);
335 identity.addActionListener(new ActionListener()
337 public void actionPerformed(ActionEvent e)
339 annotations_actionPerformed(e);
342 showGroupConsensus.addActionListener(new ActionListener()
344 public void actionPerformed(ActionEvent e)
346 annotations_actionPerformed(e);
349 showUnconserved.setFont(verdana11);
350 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
351 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
352 showUnconserved.setSelected(true);
353 showUnconserved.setText("Show Unconserved");
354 showUnconserved.addActionListener(new ActionListener()
356 public void actionPerformed(ActionEvent e)
358 showunconserved_actionPerformed(e);
361 shareSelections.setFont(verdana11);
362 shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
363 shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
364 shareSelections.setSelected(true);
365 shareSelections.setText("Share selection across views");
366 followHighlight.setFont(verdana11);
367 followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
368 followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
369 //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
370 followHighlight.setSelected(true);
371 followHighlight.setText("Scroll to highlighted regions");
373 gapLabel.setFont(verdana11);
374 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
375 gapLabel.setText("Gap Symbol ");
376 colour.setFont(verdana11);
377 colour.setBounds(new Rectangle(172, 225, 155, 21));
378 colourLabel.setFont(verdana11);
379 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
380 colourLabel.setText("Colour ");
381 fontLabel.setFont(verdana11);
382 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
383 fontLabel.setText("Font ");
384 fontSizeCB.setFont(verdana11);
385 fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
386 fontStyleCB.setFont(verdana11);
387 fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
388 fontNameCB.setFont(verdana11);
389 fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
390 gapSymbolCB.setFont(verdana11);
391 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
392 startupCheckbox.setText("Open file");
393 startupCheckbox.setFont(verdana11);
394 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
395 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
396 startupCheckbox.setSelected(true);
397 startupFileTextfield.setFont(verdana11);
398 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
399 startupFileTextfield.addMouseListener(new MouseAdapter()
401 public void mouseClicked(MouseEvent e)
403 if (e.getClickCount() > 1)
405 startupFileTextfield_mouseClicked();
410 connectTab.setLayout(gridBagLayout3);
411 serverLabel.setText("Address");
412 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
413 serverLabel.setFont(verdana11);
414 proxyServerTB.setFont(verdana11);
415 proxyPortTB.setFont(verdana11);
416 portLabel.setFont(verdana11);
417 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
418 portLabel.setText("Port");
419 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
420 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
421 browserLabel.setText("Default Browser (Unix)");
422 defaultBrowser.setFont(verdana11);
423 defaultBrowser.setText("");
424 usagestats.setText("Send usage statistics");
425 usagestats.setFont(verdana11);
426 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
427 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
428 questionnaire.setText("Check for questionnaires");
429 questionnaire.setFont(verdana11);
430 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
431 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
432 versioncheck.setText("Check for latest version");
433 versioncheck.setFont(verdana11);
434 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
435 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
436 newLink.setText("New");
437 newLink.addActionListener(new java.awt.event.ActionListener()
439 public void actionPerformed(ActionEvent e)
441 newLink_actionPerformed(e);
444 editLink.setText("Edit");
445 editLink.addActionListener(new java.awt.event.ActionListener()
447 public void actionPerformed(ActionEvent e)
449 editLink_actionPerformed(e);
452 deleteLink.setText("Delete");
453 deleteLink.addActionListener(new java.awt.event.ActionListener()
455 public void actionPerformed(ActionEvent e)
457 deleteLink_actionPerformed(e);
461 linkURLList.addListSelectionListener(new ListSelectionListener()
463 public void valueChanged(ListSelectionEvent e)
465 int index = linkURLList.getSelectedIndex();
466 linkNameList.setSelectedIndex(index);
470 linkNameList.addListSelectionListener(new ListSelectionListener()
472 public void valueChanged(ListSelectionEvent e)
474 int index = linkNameList.getSelectedIndex();
475 linkURLList.setSelectedIndex(index);
479 linkScrollPane.setBorder(null);
480 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
481 linkPanel.setLayout(borderLayout2);
482 editLinkButtons.setLayout(gridLayout1);
483 gridLayout1.setRows(3);
484 linkNameList.setFont(verdana11);
485 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
486 linkPanel2.setLayout(borderLayout3);
487 linkURLList.setFont(verdana11);
488 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
490 defaultBrowser.addMouseListener(new MouseAdapter()
492 public void mouseClicked(MouseEvent e)
494 if (e.getClickCount() > 1)
496 defaultBrowser_mouseClicked(e);
500 useProxy.setFont(verdana11);
501 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
502 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
503 useProxy.setText("Use a proxy server");
504 useProxy.addActionListener(new ActionListener()
506 public void actionPerformed(ActionEvent e)
508 useProxy_actionPerformed();
511 jPanel1.setBorder(titledBorder1);
512 jPanel1.setLayout(gridBagLayout1);
513 sortby.setFont(verdana11);
514 sortby.setBounds(new Rectangle(172, 249, 155, 21));
515 sortLabel.setFont(verdana11);
516 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
517 sortLabel.setText("Sort by ");
518 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
519 jPanel2.setLayout(gridLayout2);
520 gridLayout2.setRows(13);
521 exportTab.setLayout(null);
522 epsLabel.setFont(verdana11);
523 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
524 epsLabel.setText("EPS Rendering Style");
525 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
526 epsRendering.setFont(verdana11);
527 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
528 jLabel1.setFont(verdana11);
529 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
530 jLabel1.setText("Append /start-end (/15-380)");
531 jLabel1.setFont(verdana11);
532 fastajv.setFont(verdana11);
533 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
534 clustaljv.setText("Clustal ");
535 blcjv.setText("BLC ");
536 fastajv.setText("Fasta ");
537 msfjv.setText("MSF ");
538 pfamjv.setText("PFAM ");
539 pileupjv.setText("Pileup ");
540 msfjv.setFont(verdana11);
541 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
542 pirjv.setText("PIR ");
543 jPanel11.setFont(verdana11);
544 jPanel11.setBorder(titledBorder2);
545 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
546 jPanel11.setLayout(gridLayout3);
547 blcjv.setFont(verdana11);
548 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
549 clustaljv.setFont(verdana11);
550 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
551 pfamjv.setFont(verdana11);
552 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
553 pileupjv.setFont(verdana11);
554 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
555 pirjv.setFont(verdana11);
556 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
557 seqLimit.setFont(verdana11);
558 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
559 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
560 seqLimit.setText("Full Sequence Id");
561 gridLayout3.setRows(8);
562 smoothFont.setFont(verdana11);
563 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
564 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
565 smoothFont.setText("Smooth Font");
566 calcTab.setLayout(null);
567 autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
569 autoCalculateConsCheck.setText("AutoCalculate Consensus");
570 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
571 padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
572 padGaps.setText("Pad gaps when editing");
573 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
574 modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
575 modellerOutput.setText("Use Modeller Output");
576 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
577 dasPanel.setLayout(borderLayout4);
578 wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
579 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
580 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
581 wrap.setText("Wrap Alignment");
582 rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
583 rightAlign.setForeground(Color.black);
584 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
585 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
586 rightAlign.setText("Right Align Ids");
587 idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
588 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
589 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
590 idItalics.setText("Sequence Name Italics");
591 openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
592 openoverv.setActionCommand("Open Overview");
593 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
594 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
595 openoverv.setText("Open Overview");
596 jPanel2.add(fullScreen);
597 jPanel2.add(openoverv);
598 jPanel2.add(seqLimit);
599 jPanel2.add(rightAlign);
600 jPanel2.add(fontLabel);
601 jPanel2.add(showUnconserved);
602 jPanel2.add(idItalics);
603 jPanel2.add(smoothFont);
605 jPanel2.add(gapLabel);
606 jPanel2.add(colourLabel);
607 jPanel2.add(sortLabel);
608 jPanel2.add(startupCheckbox);
609 visualTab.add(annotations);
610 visualTab.add(startupFileTextfield);
611 visualTab.add(sortby);
612 visualTab.add(colour);
613 visualTab.add(gapSymbolCB);
614 visualTab.add(fontNameCB);
615 visualTab.add(fontSizeCB);
616 visualTab.add(fontStyleCB);
617 annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
618 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
619 annsettingsPanel.add(autoAnnotSettings1);
620 annsettingsPanel.add(autoAnnotSettings2);
621 annsettingsPanel.add(autoAnnotSettings3);
622 autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
623 autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
624 autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
625 visualTab.add(annsettingsPanel);
626 Border jb = new EmptyBorder(1,1,4,5);
627 quality.setBorder(jb);
628 conservation.setBorder(jb);
629 identity.setBorder(jb);
630 showConsensbits.setBorder(jb);
631 showGroupbits.setBorder(jb);
632 showGroupConsensus.setBorder(jb);
633 showGroupConservation.setBorder(jb);
634 showConsensHistogram.setBorder(jb);
635 showConsensLogo.setBorder(jb);
637 autoAnnotSettings2.add(conservation);
638 autoAnnotSettings1.add(quality);
639 autoAnnotSettings3.add(identity);
640 autoAnnotSettings1.add(showGroupbits);
641 autoAnnotSettings3.add(showGroupConsensus);
642 autoAnnotSettings2.add(showGroupConservation);
643 autoAnnotSettings1.add(showConsensbits);
644 autoAnnotSettings2.add(showConsensHistogram);
645 autoAnnotSettings3.add(showConsensLogo);
647 JPanel tooltipSettings = new JPanel();
648 tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
649 tooltipSettings.setBounds(173, 130, 200,62);
650 tooltipSettings.setLayout(new GridLayout(2,1));
651 tooltipSettings.add(showDbRefTooltip);
652 tooltipSettings.add(showNpTooltip);
653 visualTab.add(tooltipSettings);
654 visualTab.add(jPanel2);
656 linkPanel.add(editLinkButtons, BorderLayout.EAST);
657 editLinkButtons.add(newLink, null);
658 editLinkButtons.add(editLink, null);
659 editLinkButtons.add(deleteLink, null);
660 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
661 linkScrollPane.getViewport().add(linkPanel2, null);
662 linkPanel2.add(linkURLList, BorderLayout.CENTER);
663 linkPanel2.add(linkNameList, BorderLayout.WEST);
664 okCancelPanel.add(ok);
665 okCancelPanel.add(cancel);
666 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
668 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
669 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
670 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
672 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
673 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
675 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
676 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
677 16, 0, 0, 12), 359, -17));
678 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
679 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
680 21, 0, 35, 12), 4, 6));
681 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
682 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
683 new Insets(16, 0, 0, 0), 5, 1));
684 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
685 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
686 new Insets(0, 2, 4, 2), 54, 1));
687 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
688 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
689 new Insets(0, 2, 4, 0), 263, 1));
690 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
691 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
692 new Insets(15, 0, 0, 15), 307, 1));
693 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0,
694 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
695 new Insets(0, 2, 4,2), 70, 1));
696 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
697 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
698 new Insets(0, 2, 4,2), 70, 1));
699 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
700 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
701 new Insets(0, 2, 4,2), 70, 1));
703 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
704 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
706 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
707 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
708 gapSymbolCB.setRenderer(dlcr);
710 tabbedPane.add(visualTab, "Visual");
711 tabbedPane.add(connectTab, "Connections");
712 tabbedPane.add(exportTab, "Output");
713 jPanel11.add(jLabel1);
715 jPanel11.add(clustaljv);
716 jPanel11.add(fastajv);
718 jPanel11.add(pfamjv);
719 jPanel11.add(pileupjv);
721 exportTab.add(modellerOutput);
722 tabbedPane.add(calcTab, "Editing");
723 calcTab.add(autoCalculateConsCheck);
724 calcTab.add(padGaps);
725 tabbedPane.add(dasPanel, "DAS Settings");
727 exportTab.add(epsLabel);
728 exportTab.add(epsRendering);
729 exportTab.add(jPanel11);
732 protected void showunconserved_actionPerformed(ActionEvent e)
734 // TODO Auto-generated method stub
744 public void ok_actionPerformed(ActionEvent e)
754 public void cancel_actionPerformed(ActionEvent e)
764 public void annotations_actionPerformed(ActionEvent e)
771 public void startupFileTextfield_mouseClicked()
775 public void newLink_actionPerformed(ActionEvent e)
780 public void editLink_actionPerformed(ActionEvent e)
785 public void deleteLink_actionPerformed(ActionEvent e)
790 public void defaultBrowser_mouseClicked(MouseEvent e)
795 public void linkURLList_keyTyped(KeyEvent e)
800 public void useProxy_actionPerformed()
802 proxyServerTB.setEnabled(useProxy.isSelected());
803 proxyPortTB.setEnabled(useProxy.isSelected());