2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.jbgui;
21 import java.awt.event.*;
24 import javax.swing.border.*;
25 import javax.swing.event.*;
26 import java.awt.Rectangle;
34 public class GPreferences extends JPanel
36 JTabbedPane tabbedPane = new JTabbedPane();
38 JButton ok = new JButton();
40 JButton cancel = new JButton();
42 JPanel okCancelPanel = new JPanel();
44 BorderLayout borderLayout1 = new BorderLayout();
46 protected JCheckBox quality = new JCheckBox();
48 JPanel visualTab = new JPanel();
50 protected JCheckBox fullScreen = new JCheckBox();
52 protected JCheckBox conservation = new JCheckBox();
54 protected JCheckBox identity = new JCheckBox();
56 protected JCheckBox annotations = new JCheckBox();
58 JLabel gapLabel = new JLabel();
60 protected JComboBox colour = new JComboBox();
62 JLabel colourLabel = new JLabel();
64 JLabel fontLabel = new JLabel();
66 protected JComboBox fontSizeCB = new JComboBox();
68 protected JComboBox fontStyleCB = new JComboBox();
70 protected JComboBox fontNameCB = new JComboBox();
72 protected JComboBox gapSymbolCB = new JComboBox();
74 protected JCheckBox startupCheckbox = new JCheckBox();
76 protected JTextField startupFileTextfield = new JTextField();
78 JPanel connectTab = new JPanel();
80 JLabel serverLabel = new JLabel();
82 protected JList linkURLList = new JList();
84 protected JTextField proxyServerTB = new JTextField();
86 protected JTextField proxyPortTB = new JTextField();
88 JLabel portLabel = new JLabel();
90 JLabel browserLabel = new JLabel();
92 protected JTextField defaultBrowser = new JTextField();
94 JButton newLink = new JButton();
96 JButton editLink = new JButton();
98 JButton deleteLink = new JButton();
100 JScrollPane linkScrollPane = new JScrollPane();
102 JPanel linkPanel = new JPanel();
104 BorderLayout borderLayout2 = new BorderLayout();
106 JPanel editLinkButtons = new JPanel();
108 GridLayout gridLayout1 = new GridLayout();
110 protected JList linkNameList = new JList();
112 JPanel linkPanel2 = new JPanel();
114 BorderLayout borderLayout3 = new BorderLayout();
116 protected JCheckBox useProxy = new JCheckBox();
118 JPanel jPanel1 = new JPanel();
120 TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
122 TitledBorder titledBorder2 = new TitledBorder("File Output");
124 GridBagLayout gridBagLayout2 = new GridBagLayout();
126 GridBagLayout gridBagLayout1 = new GridBagLayout();
128 GridBagLayout gridBagLayout3 = new GridBagLayout();
130 protected JComboBox sortby = new JComboBox();
132 JLabel sortLabel = new JLabel();
134 JPanel jPanel2 = new JPanel();
136 GridLayout gridLayout2 = new GridLayout();
138 JPanel annsettingsPanel = new JPanel();
140 JPanel autoAnnotSettings1 = new JPanel();
142 JPanel autoAnnotSettings2 = new JPanel();
144 JPanel autoAnnotSettings3 = new JPanel();
146 JPanel exportTab = new JPanel();
148 JLabel epsLabel = new JLabel();
150 protected JComboBox epsRendering = new JComboBox();
152 JLabel jLabel1 = new JLabel();
154 protected JCheckBox blcjv = new JCheckBox();
156 protected JCheckBox pileupjv = new JCheckBox();
158 protected JCheckBox clustaljv = new JCheckBox();
160 protected JCheckBox msfjv = new JCheckBox();
162 protected JCheckBox fastajv = new JCheckBox();
164 protected JCheckBox pfamjv = new JCheckBox();
166 FlowLayout flowLayout1 = new FlowLayout();
168 protected JCheckBox pirjv = new JCheckBox();
170 JPanel jPanel11 = new JPanel();
172 Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
174 protected JCheckBox seqLimit = new JCheckBox();
176 GridLayout gridLayout3 = new GridLayout();
178 protected JCheckBox smoothFont = new JCheckBox();
180 JPanel calcTab = new JPanel();
182 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
184 protected JCheckBox padGaps = new JCheckBox();
186 protected JCheckBox modellerOutput = new JCheckBox();
188 protected JPanel dasPanel = new JPanel();
190 BorderLayout borderLayout4 = new BorderLayout();
192 protected JPanel wsPanel = new JPanel();
194 BorderLayout borderLayout5 = new BorderLayout();
196 protected JCheckBox wrap = new JCheckBox();
198 protected JCheckBox rightAlign = new JCheckBox();
200 protected JCheckBox showUnconserved = new JCheckBox();
202 protected JCheckBox showDbRefTooltip = new JCheckBox();
204 protected JCheckBox showNpTooltip = new JCheckBox();
206 protected JCheckBox idItalics = new JCheckBox();
208 protected JCheckBox openoverv = new JCheckBox();
210 protected JCheckBox usagestats = new JCheckBox();
212 protected JCheckBox questionnaire = new JCheckBox();
214 protected JCheckBox versioncheck = new JCheckBox();
216 protected JLabel showGroupbits = new JLabel();
218 protected JLabel showConsensbits = new JLabel();
220 protected JCheckBox showConsensLogo = new JCheckBox();
222 protected JCheckBox showConsensHistogram = new JCheckBox();
224 protected JCheckBox showGroupConsensus = new JCheckBox();
226 protected JCheckBox showGroupConservation = new JCheckBox();
228 protected JCheckBox shareSelections = new JCheckBox();
230 protected JCheckBox followHighlight = new JCheckBox();
236 * Creates a new GPreferences object.
238 public GPreferences()
243 } catch (Exception ex)
245 ex.printStackTrace();
255 private void jbInit() throws Exception
257 this.setLayout(borderLayout1);
259 ok.addActionListener(new ActionListener()
261 public void actionPerformed(ActionEvent e)
263 ok_actionPerformed(e);
266 cancel.setText("Cancel");
267 cancel.addActionListener(new ActionListener()
269 public void actionPerformed(ActionEvent e)
271 cancel_actionPerformed(e);
274 quality.setEnabled(false);
275 quality.setFont(verdana11);
276 quality.setHorizontalAlignment(SwingConstants.RIGHT);
277 quality.setHorizontalTextPosition(SwingConstants.LEFT);
278 quality.setSelected(true);
279 quality.setText("Quality");
280 visualTab.setBorder(new TitledBorder("Open new alignment"));
281 visualTab.setLayout(null);
282 fullScreen.setFont(verdana11);
283 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
284 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
285 fullScreen.setText("Maximise Window");
286 conservation.setEnabled(false);
287 conservation.setFont(verdana11);
288 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
289 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
290 conservation.setSelected(true);
291 conservation.setText("Conservation");
292 identity.setEnabled(false);
293 identity.setFont(verdana11);
294 identity.setHorizontalAlignment(SwingConstants.RIGHT);
295 identity.setHorizontalTextPosition(SwingConstants.LEFT);
296 identity.setSelected(true);
297 identity.setText("Consensus");
298 showGroupbits.setFont(verdana11);
299 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
300 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
301 showGroupbits.setText("Show group:");
302 showConsensbits.setFont(verdana11);
303 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
304 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
305 showConsensbits.setText("Consensus:");
306 showConsensHistogram.setEnabled(false);
307 showConsensHistogram.setFont(verdana11);
308 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
309 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
310 showConsensHistogram.setSelected(true);
311 showConsensHistogram.setText("Histogram");
312 showConsensLogo.setEnabled(false);
313 showConsensLogo.setFont(verdana11);
314 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
315 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
316 showConsensLogo.setSelected(true);
317 showConsensLogo.setText("Logo");
318 showGroupConsensus.setEnabled(false);
319 showGroupConsensus.setFont(verdana11);
320 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
321 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
322 showGroupConsensus.setSelected(true);
323 showGroupConsensus.setText("Consensus");
324 showGroupConservation.setEnabled(false);
325 showGroupConservation.setFont(verdana11);
326 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
327 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
328 showGroupConservation.setSelected(true);
329 showGroupConservation.setText("Conservation");
330 showNpTooltip.setEnabled(true);
331 showNpTooltip.setFont(verdana11);
332 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
333 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
334 showNpTooltip.setSelected(true);
335 showNpTooltip.setText("Non-positional Features");
336 showDbRefTooltip.setEnabled(true);
337 showDbRefTooltip.setFont(verdana11);
338 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
339 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
340 showDbRefTooltip.setSelected(true);
341 showDbRefTooltip.setText("Database References");
342 annotations.setFont(verdana11);
343 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
344 annotations.setHorizontalTextPosition(SwingConstants.LEADING);
345 annotations.setSelected(true);
346 annotations.setText("Show Annotations");
347 annotations.setBounds(new Rectangle(169, 12, 200, 23));
348 annotations.addActionListener(new ActionListener()
350 public void actionPerformed(ActionEvent e)
352 annotations_actionPerformed(e);
355 identity.addActionListener(new ActionListener()
357 public void actionPerformed(ActionEvent e)
359 annotations_actionPerformed(e);
362 showGroupConsensus.addActionListener(new ActionListener()
364 public void actionPerformed(ActionEvent e)
366 annotations_actionPerformed(e);
369 showUnconserved.setFont(verdana11);
370 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
371 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
372 showUnconserved.setSelected(true);
373 showUnconserved.setText("Show Unconserved");
374 showUnconserved.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent e)
378 showunconserved_actionPerformed(e);
381 // / TODO: fit these in to preferences panel!!!!!
382 shareSelections.setFont(verdana11);
383 shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
384 shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
385 shareSelections.setSelected(true);
386 shareSelections.setText("Share selection across views");
387 followHighlight.setFont(verdana11);
388 followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
389 followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
390 // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
391 followHighlight.setSelected(true);
392 followHighlight.setText("Scroll to highlighted regions");
394 gapLabel.setFont(verdana11);
395 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
396 gapLabel.setText("Gap Symbol ");
397 colour.setFont(verdana11);
398 colour.setBounds(new Rectangle(172, 225, 155, 21));
399 colourLabel.setFont(verdana11);
400 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
401 colourLabel.setText("Colour ");
402 fontLabel.setFont(verdana11);
403 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
404 fontLabel.setText("Font ");
405 fontSizeCB.setFont(verdana11);
406 fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
407 fontStyleCB.setFont(verdana11);
408 fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
409 fontNameCB.setFont(verdana11);
410 fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
411 gapSymbolCB.setFont(verdana11);
412 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
413 startupCheckbox.setText("Open file");
414 startupCheckbox.setFont(verdana11);
415 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
416 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
417 startupCheckbox.setSelected(true);
418 startupFileTextfield.setFont(verdana11);
419 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
420 startupFileTextfield.addMouseListener(new MouseAdapter()
422 public void mouseClicked(MouseEvent e)
424 if (e.getClickCount() > 1)
426 startupFileTextfield_mouseClicked();
431 connectTab.setLayout(gridBagLayout3);
432 serverLabel.setText("Address");
433 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
434 serverLabel.setFont(verdana11);
435 proxyServerTB.setFont(verdana11);
436 proxyPortTB.setFont(verdana11);
437 portLabel.setFont(verdana11);
438 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
439 portLabel.setText("Port");
440 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
441 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
442 browserLabel.setText("Default Browser (Unix)");
443 defaultBrowser.setFont(verdana11);
444 defaultBrowser.setText("");
445 usagestats.setText("Send usage statistics");
446 usagestats.setFont(verdana11);
447 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
448 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
449 questionnaire.setText("Check for questionnaires");
450 questionnaire.setFont(verdana11);
451 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
452 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
453 versioncheck.setText("Check for latest version");
454 versioncheck.setFont(verdana11);
455 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
456 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
457 newLink.setText("New");
458 newLink.addActionListener(new java.awt.event.ActionListener()
460 public void actionPerformed(ActionEvent e)
462 newLink_actionPerformed(e);
465 editLink.setText("Edit");
466 editLink.addActionListener(new java.awt.event.ActionListener()
468 public void actionPerformed(ActionEvent e)
470 editLink_actionPerformed(e);
473 deleteLink.setText("Delete");
474 deleteLink.addActionListener(new java.awt.event.ActionListener()
476 public void actionPerformed(ActionEvent e)
478 deleteLink_actionPerformed(e);
482 linkURLList.addListSelectionListener(new ListSelectionListener()
484 public void valueChanged(ListSelectionEvent e)
486 int index = linkURLList.getSelectedIndex();
487 linkNameList.setSelectedIndex(index);
491 linkNameList.addListSelectionListener(new ListSelectionListener()
493 public void valueChanged(ListSelectionEvent e)
495 int index = linkNameList.getSelectedIndex();
496 linkURLList.setSelectedIndex(index);
500 linkScrollPane.setBorder(null);
501 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
502 linkPanel.setLayout(borderLayout2);
503 editLinkButtons.setLayout(gridLayout1);
504 gridLayout1.setRows(3);
505 linkNameList.setFont(verdana11);
506 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
507 linkPanel2.setLayout(borderLayout3);
508 linkURLList.setFont(verdana11);
509 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
511 defaultBrowser.addMouseListener(new MouseAdapter()
513 public void mouseClicked(MouseEvent e)
515 if (e.getClickCount() > 1)
517 defaultBrowser_mouseClicked(e);
521 useProxy.setFont(verdana11);
522 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
523 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
524 useProxy.setText("Use a proxy server");
525 useProxy.addActionListener(new ActionListener()
527 public void actionPerformed(ActionEvent e)
529 useProxy_actionPerformed();
532 jPanel1.setBorder(titledBorder1);
533 jPanel1.setLayout(gridBagLayout1);
534 sortby.setFont(verdana11);
535 sortby.setBounds(new Rectangle(172, 249, 155, 21));
536 sortLabel.setFont(verdana11);
537 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
538 sortLabel.setText("Sort by ");
539 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
540 jPanel2.setLayout(gridLayout2);
541 gridLayout2.setRows(13);
542 exportTab.setLayout(null);
543 epsLabel.setFont(verdana11);
544 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
545 epsLabel.setText("EPS Rendering Style");
546 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
547 epsRendering.setFont(verdana11);
548 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
549 jLabel1.setFont(verdana11);
550 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
551 jLabel1.setText("Append /start-end (/15-380)");
552 jLabel1.setFont(verdana11);
553 fastajv.setFont(verdana11);
554 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
555 clustaljv.setText("Clustal ");
556 blcjv.setText("BLC ");
557 fastajv.setText("Fasta ");
558 msfjv.setText("MSF ");
559 pfamjv.setText("PFAM ");
560 pileupjv.setText("Pileup ");
561 msfjv.setFont(verdana11);
562 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
563 pirjv.setText("PIR ");
564 jPanel11.setFont(verdana11);
565 jPanel11.setBorder(titledBorder2);
566 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
567 jPanel11.setLayout(gridLayout3);
568 blcjv.setFont(verdana11);
569 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
570 clustaljv.setFont(verdana11);
571 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
572 pfamjv.setFont(verdana11);
573 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
574 pileupjv.setFont(verdana11);
575 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
576 pirjv.setFont(verdana11);
577 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
578 seqLimit.setFont(verdana11);
579 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
580 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
581 seqLimit.setText("Full Sequence Id");
582 gridLayout3.setRows(8);
583 smoothFont.setFont(verdana11);
584 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
585 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
586 smoothFont.setText("Smooth Font");
587 calcTab.setLayout(null);
588 autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
590 autoCalculateConsCheck.setText("AutoCalculate Consensus");
591 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
592 padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
593 padGaps.setText("Pad gaps when editing");
594 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
595 modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
596 modellerOutput.setText("Use Modeller Output");
597 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
598 dasPanel.setLayout(borderLayout4);
599 wsPanel.setLayout(borderLayout5);
600 wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
601 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
602 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
603 wrap.setText("Wrap Alignment");
604 rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
605 rightAlign.setForeground(Color.black);
606 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
607 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
608 rightAlign.setText("Right Align Ids");
609 idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
610 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
611 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
612 idItalics.setText("Sequence Name Italics");
613 openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
614 openoverv.setActionCommand("Open Overview");
615 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
616 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
617 openoverv.setText("Open Overview");
618 jPanel2.add(fullScreen);
619 jPanel2.add(openoverv);
620 jPanel2.add(seqLimit);
621 jPanel2.add(rightAlign);
622 jPanel2.add(fontLabel);
623 jPanel2.add(showUnconserved);
624 jPanel2.add(idItalics);
625 jPanel2.add(smoothFont);
627 jPanel2.add(gapLabel);
628 jPanel2.add(colourLabel);
629 jPanel2.add(sortLabel);
630 jPanel2.add(startupCheckbox);
631 visualTab.add(annotations);
632 visualTab.add(startupFileTextfield);
633 visualTab.add(sortby);
634 visualTab.add(colour);
635 visualTab.add(gapSymbolCB);
636 visualTab.add(fontNameCB);
637 visualTab.add(fontSizeCB);
638 visualTab.add(fontStyleCB);
639 annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
640 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
641 annsettingsPanel.add(autoAnnotSettings1);
642 annsettingsPanel.add(autoAnnotSettings2);
643 annsettingsPanel.add(autoAnnotSettings3);
644 autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
645 autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
646 autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
647 visualTab.add(annsettingsPanel);
648 Border jb = new EmptyBorder(1, 1, 4, 5);
649 quality.setBorder(jb);
650 conservation.setBorder(jb);
651 identity.setBorder(jb);
652 showConsensbits.setBorder(jb);
653 showGroupbits.setBorder(jb);
654 showGroupConsensus.setBorder(jb);
655 showGroupConservation.setBorder(jb);
656 showConsensHistogram.setBorder(jb);
657 showConsensLogo.setBorder(jb);
659 autoAnnotSettings2.add(conservation);
660 autoAnnotSettings1.add(quality);
661 autoAnnotSettings3.add(identity);
662 autoAnnotSettings1.add(showGroupbits);
663 autoAnnotSettings3.add(showGroupConsensus);
664 autoAnnotSettings2.add(showGroupConservation);
665 autoAnnotSettings1.add(showConsensbits);
666 autoAnnotSettings2.add(showConsensHistogram);
667 autoAnnotSettings3.add(showConsensLogo);
669 JPanel tooltipSettings = new JPanel();
670 tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
671 tooltipSettings.setBounds(173, 130, 200, 62);
672 tooltipSettings.setLayout(new GridLayout(2, 1));
673 tooltipSettings.add(showDbRefTooltip);
674 tooltipSettings.add(showNpTooltip);
675 visualTab.add(tooltipSettings);
676 visualTab.add(jPanel2);
678 linkPanel.add(editLinkButtons, BorderLayout.EAST);
679 editLinkButtons.add(newLink, null);
680 editLinkButtons.add(editLink, null);
681 editLinkButtons.add(deleteLink, null);
682 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
683 linkScrollPane.getViewport().add(linkPanel2, null);
684 linkPanel2.add(linkURLList, BorderLayout.CENTER);
685 linkPanel2.add(linkNameList, BorderLayout.WEST);
686 okCancelPanel.add(ok);
687 okCancelPanel.add(cancel);
688 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
690 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
691 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
692 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
694 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
695 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
697 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
698 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
699 16, 0, 0, 12), 359, -17));
700 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
701 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
702 21, 0, 35, 12), 4, 6));
703 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
704 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
705 new Insets(16, 0, 0, 0), 5, 1));
706 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
707 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
708 new Insets(0, 2, 4, 2), 54, 1));
709 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
710 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
711 new Insets(0, 2, 4, 0), 263, 1));
712 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
713 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
714 new Insets(15, 0, 0, 15), 307, 1));
715 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
716 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
717 new Insets(0, 2, 4, 2), 70, 1));
718 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
719 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
720 new Insets(0, 2, 4, 2), 70, 1));
721 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
722 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
723 new Insets(0, 2, 4, 2), 70, 1));
725 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
726 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
728 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
729 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
730 gapSymbolCB.setRenderer(dlcr);
732 tabbedPane.add(visualTab, "Visual");
733 tabbedPane.add(connectTab, "Connections");
734 tabbedPane.add(exportTab, "Output");
735 jPanel11.add(jLabel1);
737 jPanel11.add(clustaljv);
738 jPanel11.add(fastajv);
740 jPanel11.add(pfamjv);
741 jPanel11.add(pileupjv);
743 exportTab.add(modellerOutput);
744 tabbedPane.add(calcTab, "Editing");
745 calcTab.add(autoCalculateConsCheck);
746 calcTab.add(padGaps);
747 tabbedPane.add(dasPanel, "DAS Settings");
748 tabbedPane.add(wsPanel, "Web Services");
750 exportTab.add(epsLabel);
751 exportTab.add(epsRendering);
752 exportTab.add(jPanel11);
755 protected void showunconserved_actionPerformed(ActionEvent e)
757 // TODO Auto-generated method stub
767 public void ok_actionPerformed(ActionEvent e)
777 public void cancel_actionPerformed(ActionEvent e)
787 public void annotations_actionPerformed(ActionEvent e)
794 public void startupFileTextfield_mouseClicked()
798 public void newLink_actionPerformed(ActionEvent e)
803 public void editLink_actionPerformed(ActionEvent e)
808 public void deleteLink_actionPerformed(ActionEvent e)
813 public void defaultBrowser_mouseClicked(MouseEvent e)
818 public void linkURLList_keyTyped(KeyEvent e)
823 public void useProxy_actionPerformed()
825 proxyServerTB.setEnabled(useProxy.isSelected());
826 proxyPortTB.setEnabled(useProxy.isSelected());