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 JCheckBox wrap = new JCheckBox();
194 protected JCheckBox rightAlign = new JCheckBox();
196 protected JCheckBox showUnconserved = new JCheckBox();
198 protected JCheckBox showDbRefTooltip = new JCheckBox();
200 protected JCheckBox showNpTooltip = new JCheckBox();
202 protected JCheckBox idItalics = new JCheckBox();
204 protected JCheckBox openoverv = new JCheckBox();
206 protected JCheckBox usagestats = new JCheckBox();
208 protected JCheckBox questionnaire = new JCheckBox();
210 protected JCheckBox versioncheck = new JCheckBox();
212 protected JLabel showGroupbits = new JLabel();
214 protected JLabel showConsensbits = new JLabel();
216 protected JCheckBox showConsensLogo = new JCheckBox();
218 protected JCheckBox showConsensHistogram = new JCheckBox();
220 protected JCheckBox showGroupConsensus = new JCheckBox();
222 protected JCheckBox showGroupConservation = new JCheckBox();
224 protected JCheckBox shareSelections = new JCheckBox();
226 protected JCheckBox followHighlight = new JCheckBox();
229 * Creates a new GPreferences object.
231 public GPreferences()
236 } catch (Exception ex)
238 ex.printStackTrace();
248 private void jbInit() throws Exception
250 this.setLayout(borderLayout1);
252 ok.addActionListener(new ActionListener()
254 public void actionPerformed(ActionEvent e)
256 ok_actionPerformed(e);
259 cancel.setText("Cancel");
260 cancel.addActionListener(new ActionListener()
262 public void actionPerformed(ActionEvent e)
264 cancel_actionPerformed(e);
267 quality.setEnabled(false);
268 quality.setFont(verdana11);
269 quality.setHorizontalAlignment(SwingConstants.RIGHT);
270 quality.setHorizontalTextPosition(SwingConstants.LEFT);
271 quality.setSelected(true);
272 quality.setText("Quality");
273 visualTab.setBorder(new TitledBorder("Open new alignment"));
274 visualTab.setLayout(null);
275 fullScreen.setFont(verdana11);
276 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
277 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
278 fullScreen.setText("Maximise Window");
279 conservation.setEnabled(false);
280 conservation.setFont(verdana11);
281 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
282 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
283 conservation.setSelected(true);
284 conservation.setText("Conservation");
285 identity.setEnabled(false);
286 identity.setFont(verdana11);
287 identity.setHorizontalAlignment(SwingConstants.RIGHT);
288 identity.setHorizontalTextPosition(SwingConstants.LEFT);
289 identity.setSelected(true);
290 identity.setText("Consensus");
291 showGroupbits.setFont(verdana11);
292 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
293 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
294 showGroupbits.setText("Show group:");
295 showConsensbits.setFont(verdana11);
296 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
297 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
298 showConsensbits.setText("Consensus:");
299 showConsensHistogram.setEnabled(false);
300 showConsensHistogram.setFont(verdana11);
301 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
302 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
303 showConsensHistogram.setSelected(true);
304 showConsensHistogram.setText("Histogram");
305 showConsensLogo.setEnabled(false);
306 showConsensLogo.setFont(verdana11);
307 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
308 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
309 showConsensLogo.setSelected(true);
310 showConsensLogo.setText("Logo");
311 showGroupConsensus.setEnabled(false);
312 showGroupConsensus.setFont(verdana11);
313 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
314 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
315 showGroupConsensus.setSelected(true);
316 showGroupConsensus.setText("Consensus");
317 showGroupConservation.setEnabled(false);
318 showGroupConservation.setFont(verdana11);
319 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
320 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
321 showGroupConservation.setSelected(true);
322 showGroupConservation.setText("Conservation");
323 showNpTooltip.setEnabled(true);
324 showNpTooltip.setFont(verdana11);
325 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
326 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
327 showNpTooltip.setSelected(true);
328 showNpTooltip.setText("Non-positional Features");
329 showDbRefTooltip.setEnabled(true);
330 showDbRefTooltip.setFont(verdana11);
331 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
332 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
333 showDbRefTooltip.setSelected(true);
334 showDbRefTooltip.setText("Database References");
335 annotations.setFont(verdana11);
336 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
337 annotations.setHorizontalTextPosition(SwingConstants.LEADING);
338 annotations.setSelected(true);
339 annotations.setText("Show Annotations");
340 annotations.setBounds(new Rectangle(169, 12, 200, 23));
341 annotations.addActionListener(new ActionListener()
343 public void actionPerformed(ActionEvent e)
345 annotations_actionPerformed(e);
348 identity.addActionListener(new ActionListener()
350 public void actionPerformed(ActionEvent e)
352 annotations_actionPerformed(e);
355 showGroupConsensus.addActionListener(new ActionListener()
357 public void actionPerformed(ActionEvent e)
359 annotations_actionPerformed(e);
362 showUnconserved.setFont(verdana11);
363 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
364 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
365 showUnconserved.setSelected(true);
366 showUnconserved.setText("Show Unconserved");
367 showUnconserved.addActionListener(new ActionListener()
369 public void actionPerformed(ActionEvent e)
371 showunconserved_actionPerformed(e);
374 // / TODO: fit these in to preferences panel!!!!!
375 shareSelections.setFont(verdana11);
376 shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
377 shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
378 shareSelections.setSelected(true);
379 shareSelections.setText("Share selection across views");
380 followHighlight.setFont(verdana11);
381 followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
382 followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
383 // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
384 followHighlight.setSelected(true);
385 followHighlight.setText("Scroll to highlighted regions");
387 gapLabel.setFont(verdana11);
388 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
389 gapLabel.setText("Gap Symbol ");
390 colour.setFont(verdana11);
391 colour.setBounds(new Rectangle(172, 225, 155, 21));
392 colourLabel.setFont(verdana11);
393 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
394 colourLabel.setText("Colour ");
395 fontLabel.setFont(verdana11);
396 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
397 fontLabel.setText("Font ");
398 fontSizeCB.setFont(verdana11);
399 fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
400 fontStyleCB.setFont(verdana11);
401 fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
402 fontNameCB.setFont(verdana11);
403 fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
404 gapSymbolCB.setFont(verdana11);
405 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
406 startupCheckbox.setText("Open file");
407 startupCheckbox.setFont(verdana11);
408 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
409 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
410 startupCheckbox.setSelected(true);
411 startupFileTextfield.setFont(verdana11);
412 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
413 startupFileTextfield.addMouseListener(new MouseAdapter()
415 public void mouseClicked(MouseEvent e)
417 if (e.getClickCount() > 1)
419 startupFileTextfield_mouseClicked();
424 connectTab.setLayout(gridBagLayout3);
425 serverLabel.setText("Address");
426 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
427 serverLabel.setFont(verdana11);
428 proxyServerTB.setFont(verdana11);
429 proxyPortTB.setFont(verdana11);
430 portLabel.setFont(verdana11);
431 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
432 portLabel.setText("Port");
433 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
434 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
435 browserLabel.setText("Default Browser (Unix)");
436 defaultBrowser.setFont(verdana11);
437 defaultBrowser.setText("");
438 usagestats.setText("Send usage statistics");
439 usagestats.setFont(verdana11);
440 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
441 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
442 questionnaire.setText("Check for questionnaires");
443 questionnaire.setFont(verdana11);
444 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
445 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
446 versioncheck.setText("Check for latest version");
447 versioncheck.setFont(verdana11);
448 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
449 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
450 newLink.setText("New");
451 newLink.addActionListener(new java.awt.event.ActionListener()
453 public void actionPerformed(ActionEvent e)
455 newLink_actionPerformed(e);
458 editLink.setText("Edit");
459 editLink.addActionListener(new java.awt.event.ActionListener()
461 public void actionPerformed(ActionEvent e)
463 editLink_actionPerformed(e);
466 deleteLink.setText("Delete");
467 deleteLink.addActionListener(new java.awt.event.ActionListener()
469 public void actionPerformed(ActionEvent e)
471 deleteLink_actionPerformed(e);
475 linkURLList.addListSelectionListener(new ListSelectionListener()
477 public void valueChanged(ListSelectionEvent e)
479 int index = linkURLList.getSelectedIndex();
480 linkNameList.setSelectedIndex(index);
484 linkNameList.addListSelectionListener(new ListSelectionListener()
486 public void valueChanged(ListSelectionEvent e)
488 int index = linkNameList.getSelectedIndex();
489 linkURLList.setSelectedIndex(index);
493 linkScrollPane.setBorder(null);
494 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
495 linkPanel.setLayout(borderLayout2);
496 editLinkButtons.setLayout(gridLayout1);
497 gridLayout1.setRows(3);
498 linkNameList.setFont(verdana11);
499 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
500 linkPanel2.setLayout(borderLayout3);
501 linkURLList.setFont(verdana11);
502 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
504 defaultBrowser.addMouseListener(new MouseAdapter()
506 public void mouseClicked(MouseEvent e)
508 if (e.getClickCount() > 1)
510 defaultBrowser_mouseClicked(e);
514 useProxy.setFont(verdana11);
515 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
516 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
517 useProxy.setText("Use a proxy server");
518 useProxy.addActionListener(new ActionListener()
520 public void actionPerformed(ActionEvent e)
522 useProxy_actionPerformed();
525 jPanel1.setBorder(titledBorder1);
526 jPanel1.setLayout(gridBagLayout1);
527 sortby.setFont(verdana11);
528 sortby.setBounds(new Rectangle(172, 249, 155, 21));
529 sortLabel.setFont(verdana11);
530 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
531 sortLabel.setText("Sort by ");
532 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
533 jPanel2.setLayout(gridLayout2);
534 gridLayout2.setRows(13);
535 exportTab.setLayout(null);
536 epsLabel.setFont(verdana11);
537 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
538 epsLabel.setText("EPS Rendering Style");
539 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
540 epsRendering.setFont(verdana11);
541 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
542 jLabel1.setFont(verdana11);
543 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
544 jLabel1.setText("Append /start-end (/15-380)");
545 jLabel1.setFont(verdana11);
546 fastajv.setFont(verdana11);
547 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
548 clustaljv.setText("Clustal ");
549 blcjv.setText("BLC ");
550 fastajv.setText("Fasta ");
551 msfjv.setText("MSF ");
552 pfamjv.setText("PFAM ");
553 pileupjv.setText("Pileup ");
554 msfjv.setFont(verdana11);
555 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
556 pirjv.setText("PIR ");
557 jPanel11.setFont(verdana11);
558 jPanel11.setBorder(titledBorder2);
559 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
560 jPanel11.setLayout(gridLayout3);
561 blcjv.setFont(verdana11);
562 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
563 clustaljv.setFont(verdana11);
564 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
565 pfamjv.setFont(verdana11);
566 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
567 pileupjv.setFont(verdana11);
568 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
569 pirjv.setFont(verdana11);
570 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
571 seqLimit.setFont(verdana11);
572 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
573 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
574 seqLimit.setText("Full Sequence Id");
575 gridLayout3.setRows(8);
576 smoothFont.setFont(verdana11);
577 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
578 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
579 smoothFont.setText("Smooth Font");
580 calcTab.setLayout(null);
581 autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
583 autoCalculateConsCheck.setText("AutoCalculate Consensus");
584 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
585 padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
586 padGaps.setText("Pad gaps when editing");
587 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
588 modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
589 modellerOutput.setText("Use Modeller Output");
590 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
591 dasPanel.setLayout(borderLayout4);
592 wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
593 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
594 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
595 wrap.setText("Wrap Alignment");
596 rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
597 rightAlign.setForeground(Color.black);
598 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
599 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
600 rightAlign.setText("Right Align Ids");
601 idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
602 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
603 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
604 idItalics.setText("Sequence Name Italics");
605 openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
606 openoverv.setActionCommand("Open Overview");
607 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
608 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
609 openoverv.setText("Open Overview");
610 jPanel2.add(fullScreen);
611 jPanel2.add(openoverv);
612 jPanel2.add(seqLimit);
613 jPanel2.add(rightAlign);
614 jPanel2.add(fontLabel);
615 jPanel2.add(showUnconserved);
616 jPanel2.add(idItalics);
617 jPanel2.add(smoothFont);
619 jPanel2.add(gapLabel);
620 jPanel2.add(colourLabel);
621 jPanel2.add(sortLabel);
622 jPanel2.add(startupCheckbox);
623 visualTab.add(annotations);
624 visualTab.add(startupFileTextfield);
625 visualTab.add(sortby);
626 visualTab.add(colour);
627 visualTab.add(gapSymbolCB);
628 visualTab.add(fontNameCB);
629 visualTab.add(fontSizeCB);
630 visualTab.add(fontStyleCB);
631 annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
632 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
633 annsettingsPanel.add(autoAnnotSettings1);
634 annsettingsPanel.add(autoAnnotSettings2);
635 annsettingsPanel.add(autoAnnotSettings3);
636 autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
637 autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
638 autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
639 visualTab.add(annsettingsPanel);
640 Border jb = new EmptyBorder(1, 1, 4, 5);
641 quality.setBorder(jb);
642 conservation.setBorder(jb);
643 identity.setBorder(jb);
644 showConsensbits.setBorder(jb);
645 showGroupbits.setBorder(jb);
646 showGroupConsensus.setBorder(jb);
647 showGroupConservation.setBorder(jb);
648 showConsensHistogram.setBorder(jb);
649 showConsensLogo.setBorder(jb);
651 autoAnnotSettings2.add(conservation);
652 autoAnnotSettings1.add(quality);
653 autoAnnotSettings3.add(identity);
654 autoAnnotSettings1.add(showGroupbits);
655 autoAnnotSettings3.add(showGroupConsensus);
656 autoAnnotSettings2.add(showGroupConservation);
657 autoAnnotSettings1.add(showConsensbits);
658 autoAnnotSettings2.add(showConsensHistogram);
659 autoAnnotSettings3.add(showConsensLogo);
661 JPanel tooltipSettings = new JPanel();
662 tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
663 tooltipSettings.setBounds(173, 130, 200, 62);
664 tooltipSettings.setLayout(new GridLayout(2, 1));
665 tooltipSettings.add(showDbRefTooltip);
666 tooltipSettings.add(showNpTooltip);
667 visualTab.add(tooltipSettings);
668 visualTab.add(jPanel2);
670 linkPanel.add(editLinkButtons, BorderLayout.EAST);
671 editLinkButtons.add(newLink, null);
672 editLinkButtons.add(editLink, null);
673 editLinkButtons.add(deleteLink, null);
674 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
675 linkScrollPane.getViewport().add(linkPanel2, null);
676 linkPanel2.add(linkURLList, BorderLayout.CENTER);
677 linkPanel2.add(linkNameList, BorderLayout.WEST);
678 okCancelPanel.add(ok);
679 okCancelPanel.add(cancel);
680 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
682 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
683 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
684 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
686 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
687 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
689 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
690 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
691 16, 0, 0, 12), 359, -17));
692 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
693 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
694 21, 0, 35, 12), 4, 6));
695 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
696 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
697 new Insets(16, 0, 0, 0), 5, 1));
698 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
699 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
700 new Insets(0, 2, 4, 2), 54, 1));
701 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
702 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
703 new Insets(0, 2, 4, 0), 263, 1));
704 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
705 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
706 new Insets(15, 0, 0, 15), 307, 1));
707 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
708 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
709 new Insets(0, 2, 4, 2), 70, 1));
710 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
711 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
712 new Insets(0, 2, 4, 2), 70, 1));
713 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
714 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
715 new Insets(0, 2, 4, 2), 70, 1));
717 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
718 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
720 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
721 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
722 gapSymbolCB.setRenderer(dlcr);
724 tabbedPane.add(visualTab, "Visual");
725 tabbedPane.add(connectTab, "Connections");
726 tabbedPane.add(exportTab, "Output");
727 jPanel11.add(jLabel1);
729 jPanel11.add(clustaljv);
730 jPanel11.add(fastajv);
732 jPanel11.add(pfamjv);
733 jPanel11.add(pileupjv);
735 exportTab.add(modellerOutput);
736 tabbedPane.add(calcTab, "Editing");
737 calcTab.add(autoCalculateConsCheck);
738 calcTab.add(padGaps);
739 tabbedPane.add(dasPanel, "DAS Settings");
741 exportTab.add(epsLabel);
742 exportTab.add(epsRendering);
743 exportTab.add(jPanel11);
746 protected void showunconserved_actionPerformed(ActionEvent e)
748 // TODO Auto-generated method stub
758 public void ok_actionPerformed(ActionEvent e)
768 public void cancel_actionPerformed(ActionEvent e)
778 public void annotations_actionPerformed(ActionEvent e)
785 public void startupFileTextfield_mouseClicked()
789 public void newLink_actionPerformed(ActionEvent e)
794 public void editLink_actionPerformed(ActionEvent e)
799 public void deleteLink_actionPerformed(ActionEvent e)
804 public void defaultBrowser_mouseClicked(MouseEvent e)
809 public void linkURLList_keyTyped(KeyEvent e)
814 public void useProxy_actionPerformed()
816 proxyServerTB.setEnabled(useProxy.isSelected());
817 proxyPortTB.setEnabled(useProxy.isSelected());