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 /// TODO: fit these in to preferences panel!!!!!
362 shareSelections.setFont(verdana11);
363 shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
364 shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
365 shareSelections.setSelected(true);
366 shareSelections.setText("Share selection across views");
367 followHighlight.setFont(verdana11);
368 followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
369 followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
370 //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
371 followHighlight.setSelected(true);
372 followHighlight.setText("Scroll to highlighted regions");
374 gapLabel.setFont(verdana11);
375 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
376 gapLabel.setText("Gap Symbol ");
377 colour.setFont(verdana11);
378 colour.setBounds(new Rectangle(172, 225, 155, 21));
379 colourLabel.setFont(verdana11);
380 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
381 colourLabel.setText("Colour ");
382 fontLabel.setFont(verdana11);
383 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
384 fontLabel.setText("Font ");
385 fontSizeCB.setFont(verdana11);
386 fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
387 fontStyleCB.setFont(verdana11);
388 fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
389 fontNameCB.setFont(verdana11);
390 fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
391 gapSymbolCB.setFont(verdana11);
392 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
393 startupCheckbox.setText("Open file");
394 startupCheckbox.setFont(verdana11);
395 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
396 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
397 startupCheckbox.setSelected(true);
398 startupFileTextfield.setFont(verdana11);
399 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
400 startupFileTextfield.addMouseListener(new MouseAdapter()
402 public void mouseClicked(MouseEvent e)
404 if (e.getClickCount() > 1)
406 startupFileTextfield_mouseClicked();
411 connectTab.setLayout(gridBagLayout3);
412 serverLabel.setText("Address");
413 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
414 serverLabel.setFont(verdana11);
415 proxyServerTB.setFont(verdana11);
416 proxyPortTB.setFont(verdana11);
417 portLabel.setFont(verdana11);
418 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
419 portLabel.setText("Port");
420 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
421 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
422 browserLabel.setText("Default Browser (Unix)");
423 defaultBrowser.setFont(verdana11);
424 defaultBrowser.setText("");
425 usagestats.setText("Send usage statistics");
426 usagestats.setFont(verdana11);
427 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
428 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
429 questionnaire.setText("Check for questionnaires");
430 questionnaire.setFont(verdana11);
431 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
432 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
433 versioncheck.setText("Check for latest version");
434 versioncheck.setFont(verdana11);
435 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
436 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
437 newLink.setText("New");
438 newLink.addActionListener(new java.awt.event.ActionListener()
440 public void actionPerformed(ActionEvent e)
442 newLink_actionPerformed(e);
445 editLink.setText("Edit");
446 editLink.addActionListener(new java.awt.event.ActionListener()
448 public void actionPerformed(ActionEvent e)
450 editLink_actionPerformed(e);
453 deleteLink.setText("Delete");
454 deleteLink.addActionListener(new java.awt.event.ActionListener()
456 public void actionPerformed(ActionEvent e)
458 deleteLink_actionPerformed(e);
462 linkURLList.addListSelectionListener(new ListSelectionListener()
464 public void valueChanged(ListSelectionEvent e)
466 int index = linkURLList.getSelectedIndex();
467 linkNameList.setSelectedIndex(index);
471 linkNameList.addListSelectionListener(new ListSelectionListener()
473 public void valueChanged(ListSelectionEvent e)
475 int index = linkNameList.getSelectedIndex();
476 linkURLList.setSelectedIndex(index);
480 linkScrollPane.setBorder(null);
481 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
482 linkPanel.setLayout(borderLayout2);
483 editLinkButtons.setLayout(gridLayout1);
484 gridLayout1.setRows(3);
485 linkNameList.setFont(verdana11);
486 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
487 linkPanel2.setLayout(borderLayout3);
488 linkURLList.setFont(verdana11);
489 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
491 defaultBrowser.addMouseListener(new MouseAdapter()
493 public void mouseClicked(MouseEvent e)
495 if (e.getClickCount() > 1)
497 defaultBrowser_mouseClicked(e);
501 useProxy.setFont(verdana11);
502 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
503 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
504 useProxy.setText("Use a proxy server");
505 useProxy.addActionListener(new ActionListener()
507 public void actionPerformed(ActionEvent e)
509 useProxy_actionPerformed();
512 jPanel1.setBorder(titledBorder1);
513 jPanel1.setLayout(gridBagLayout1);
514 sortby.setFont(verdana11);
515 sortby.setBounds(new Rectangle(172, 249, 155, 21));
516 sortLabel.setFont(verdana11);
517 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
518 sortLabel.setText("Sort by ");
519 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
520 jPanel2.setLayout(gridLayout2);
521 gridLayout2.setRows(13);
522 exportTab.setLayout(null);
523 epsLabel.setFont(verdana11);
524 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
525 epsLabel.setText("EPS Rendering Style");
526 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
527 epsRendering.setFont(verdana11);
528 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
529 jLabel1.setFont(verdana11);
530 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
531 jLabel1.setText("Append /start-end (/15-380)");
532 jLabel1.setFont(verdana11);
533 fastajv.setFont(verdana11);
534 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
535 clustaljv.setText("Clustal ");
536 blcjv.setText("BLC ");
537 fastajv.setText("Fasta ");
538 msfjv.setText("MSF ");
539 pfamjv.setText("PFAM ");
540 pileupjv.setText("Pileup ");
541 msfjv.setFont(verdana11);
542 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
543 pirjv.setText("PIR ");
544 jPanel11.setFont(verdana11);
545 jPanel11.setBorder(titledBorder2);
546 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
547 jPanel11.setLayout(gridLayout3);
548 blcjv.setFont(verdana11);
549 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
550 clustaljv.setFont(verdana11);
551 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
552 pfamjv.setFont(verdana11);
553 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
554 pileupjv.setFont(verdana11);
555 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
556 pirjv.setFont(verdana11);
557 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
558 seqLimit.setFont(verdana11);
559 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
560 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
561 seqLimit.setText("Full Sequence Id");
562 gridLayout3.setRows(8);
563 smoothFont.setFont(verdana11);
564 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
565 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
566 smoothFont.setText("Smooth Font");
567 calcTab.setLayout(null);
568 autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
570 autoCalculateConsCheck.setText("AutoCalculate Consensus");
571 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
572 padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
573 padGaps.setText("Pad gaps when editing");
574 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
575 modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
576 modellerOutput.setText("Use Modeller Output");
577 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
578 dasPanel.setLayout(borderLayout4);
579 wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
580 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
581 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
582 wrap.setText("Wrap Alignment");
583 rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
584 rightAlign.setForeground(Color.black);
585 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
586 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
587 rightAlign.setText("Right Align Ids");
588 idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
589 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
590 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
591 idItalics.setText("Sequence Name Italics");
592 openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
593 openoverv.setActionCommand("Open Overview");
594 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
595 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
596 openoverv.setText("Open Overview");
597 jPanel2.add(fullScreen);
598 jPanel2.add(openoverv);
599 jPanel2.add(seqLimit);
600 jPanel2.add(rightAlign);
601 jPanel2.add(fontLabel);
602 jPanel2.add(showUnconserved);
603 jPanel2.add(idItalics);
604 jPanel2.add(smoothFont);
606 jPanel2.add(gapLabel);
607 jPanel2.add(colourLabel);
608 jPanel2.add(sortLabel);
609 jPanel2.add(startupCheckbox);
610 visualTab.add(annotations);
611 visualTab.add(startupFileTextfield);
612 visualTab.add(sortby);
613 visualTab.add(colour);
614 visualTab.add(gapSymbolCB);
615 visualTab.add(fontNameCB);
616 visualTab.add(fontSizeCB);
617 visualTab.add(fontStyleCB);
618 annsettingsPanel.setBounds(new Rectangle(173,37,300,62));
619 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
620 annsettingsPanel.add(autoAnnotSettings1);
621 annsettingsPanel.add(autoAnnotSettings2);
622 annsettingsPanel.add(autoAnnotSettings3);
623 autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
624 autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
625 autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
626 visualTab.add(annsettingsPanel);
627 Border jb = new EmptyBorder(1,1,4,5);
628 quality.setBorder(jb);
629 conservation.setBorder(jb);
630 identity.setBorder(jb);
631 showConsensbits.setBorder(jb);
632 showGroupbits.setBorder(jb);
633 showGroupConsensus.setBorder(jb);
634 showGroupConservation.setBorder(jb);
635 showConsensHistogram.setBorder(jb);
636 showConsensLogo.setBorder(jb);
638 autoAnnotSettings2.add(conservation);
639 autoAnnotSettings1.add(quality);
640 autoAnnotSettings3.add(identity);
641 autoAnnotSettings1.add(showGroupbits);
642 autoAnnotSettings3.add(showGroupConsensus);
643 autoAnnotSettings2.add(showGroupConservation);
644 autoAnnotSettings1.add(showConsensbits);
645 autoAnnotSettings2.add(showConsensHistogram);
646 autoAnnotSettings3.add(showConsensLogo);
648 JPanel tooltipSettings = new JPanel();
649 tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
650 tooltipSettings.setBounds(173, 130, 200,62);
651 tooltipSettings.setLayout(new GridLayout(2,1));
652 tooltipSettings.add(showDbRefTooltip);
653 tooltipSettings.add(showNpTooltip);
654 visualTab.add(tooltipSettings);
655 visualTab.add(jPanel2);
657 linkPanel.add(editLinkButtons, BorderLayout.EAST);
658 editLinkButtons.add(newLink, null);
659 editLinkButtons.add(editLink, null);
660 editLinkButtons.add(deleteLink, null);
661 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
662 linkScrollPane.getViewport().add(linkPanel2, null);
663 linkPanel2.add(linkURLList, BorderLayout.CENTER);
664 linkPanel2.add(linkNameList, BorderLayout.WEST);
665 okCancelPanel.add(ok);
666 okCancelPanel.add(cancel);
667 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
669 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
670 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
671 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
673 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
674 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
676 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
677 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
678 16, 0, 0, 12), 359, -17));
679 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
680 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
681 21, 0, 35, 12), 4, 6));
682 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
683 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
684 new Insets(16, 0, 0, 0), 5, 1));
685 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
686 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
687 new Insets(0, 2, 4, 2), 54, 1));
688 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
689 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
690 new Insets(0, 2, 4, 0), 263, 1));
691 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
692 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
693 new Insets(15, 0, 0, 15), 307, 1));
694 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0,
695 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
696 new Insets(0, 2, 4,2), 70, 1));
697 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
698 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
699 new Insets(0, 2, 4,2), 70, 1));
700 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
701 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
702 new Insets(0, 2, 4,2), 70, 1));
704 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
705 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
707 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
708 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
709 gapSymbolCB.setRenderer(dlcr);
711 tabbedPane.add(visualTab, "Visual");
712 tabbedPane.add(connectTab, "Connections");
713 tabbedPane.add(exportTab, "Output");
714 jPanel11.add(jLabel1);
716 jPanel11.add(clustaljv);
717 jPanel11.add(fastajv);
719 jPanel11.add(pfamjv);
720 jPanel11.add(pileupjv);
722 exportTab.add(modellerOutput);
723 tabbedPane.add(calcTab, "Editing");
724 calcTab.add(autoCalculateConsCheck);
725 calcTab.add(padGaps);
726 tabbedPane.add(dasPanel, "DAS Settings");
728 exportTab.add(epsLabel);
729 exportTab.add(epsRendering);
730 exportTab.add(jPanel11);
733 protected void showunconserved_actionPerformed(ActionEvent e)
735 // TODO Auto-generated method stub
745 public void ok_actionPerformed(ActionEvent e)
755 public void cancel_actionPerformed(ActionEvent e)
765 public void annotations_actionPerformed(ActionEvent e)
772 public void startupFileTextfield_mouseClicked()
776 public void newLink_actionPerformed(ActionEvent e)
781 public void editLink_actionPerformed(ActionEvent e)
786 public void deleteLink_actionPerformed(ActionEvent e)
791 public void defaultBrowser_mouseClicked(MouseEvent e)
796 public void linkURLList_keyTyped(KeyEvent e)
801 public void useProxy_actionPerformed()
803 proxyServerTB.setEnabled(useProxy.isSelected());
804 proxyPortTB.setEnabled(useProxy.isSelected());