2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
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();
233 * Creates a new GPreferences object.
235 public GPreferences()
240 } catch (Exception ex)
242 ex.printStackTrace();
252 private void jbInit() throws Exception
254 this.setLayout(borderLayout1);
256 ok.addActionListener(new ActionListener()
258 public void actionPerformed(ActionEvent e)
260 ok_actionPerformed(e);
263 cancel.setText("Cancel");
264 cancel.addActionListener(new ActionListener()
266 public void actionPerformed(ActionEvent e)
268 cancel_actionPerformed(e);
271 quality.setEnabled(false);
272 quality.setFont(verdana11);
273 quality.setHorizontalAlignment(SwingConstants.RIGHT);
274 quality.setHorizontalTextPosition(SwingConstants.LEFT);
275 quality.setSelected(true);
276 quality.setText("Quality");
277 visualTab.setBorder(new TitledBorder("Open new alignment"));
278 visualTab.setLayout(null);
279 fullScreen.setFont(verdana11);
280 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
281 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
282 fullScreen.setText("Maximise Window");
283 conservation.setEnabled(false);
284 conservation.setFont(verdana11);
285 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
286 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
287 conservation.setSelected(true);
288 conservation.setText("Conservation");
289 identity.setEnabled(false);
290 identity.setFont(verdana11);
291 identity.setHorizontalAlignment(SwingConstants.RIGHT);
292 identity.setHorizontalTextPosition(SwingConstants.LEFT);
293 identity.setSelected(true);
294 identity.setText("Consensus");
295 showGroupbits.setFont(verdana11);
296 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
297 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
298 showGroupbits.setText("Show group:");
299 showConsensbits.setFont(verdana11);
300 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
301 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
302 showConsensbits.setText("Consensus:");
303 showConsensHistogram.setEnabled(false);
304 showConsensHistogram.setFont(verdana11);
305 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
306 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
307 showConsensHistogram.setSelected(true);
308 showConsensHistogram.setText("Histogram");
309 showConsensLogo.setEnabled(false);
310 showConsensLogo.setFont(verdana11);
311 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
312 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
313 showConsensLogo.setSelected(true);
314 showConsensLogo.setText("Logo");
315 showGroupConsensus.setEnabled(false);
316 showGroupConsensus.setFont(verdana11);
317 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
318 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
319 showGroupConsensus.setSelected(true);
320 showGroupConsensus.setText("Consensus");
321 showGroupConservation.setEnabled(false);
322 showGroupConservation.setFont(verdana11);
323 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
324 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
325 showGroupConservation.setSelected(true);
326 showGroupConservation.setText("Conservation");
327 showNpTooltip.setEnabled(true);
328 showNpTooltip.setFont(verdana11);
329 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
330 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
331 showNpTooltip.setSelected(true);
332 showNpTooltip.setText("Non-positional Features");
333 showDbRefTooltip.setEnabled(true);
334 showDbRefTooltip.setFont(verdana11);
335 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
336 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
337 showDbRefTooltip.setSelected(true);
338 showDbRefTooltip.setText("Database References");
339 annotations.setFont(verdana11);
340 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
341 annotations.setHorizontalTextPosition(SwingConstants.LEADING);
342 annotations.setSelected(true);
343 annotations.setText("Show Annotations");
344 annotations.setBounds(new Rectangle(169, 12, 200, 23));
345 annotations.addActionListener(new ActionListener()
347 public void actionPerformed(ActionEvent e)
349 annotations_actionPerformed(e);
352 identity.addActionListener(new ActionListener()
354 public void actionPerformed(ActionEvent e)
356 annotations_actionPerformed(e);
359 showGroupConsensus.addActionListener(new ActionListener()
361 public void actionPerformed(ActionEvent e)
363 annotations_actionPerformed(e);
366 showUnconserved.setFont(verdana11);
367 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
368 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
369 showUnconserved.setSelected(true);
370 showUnconserved.setText("Show Unconserved");
371 showUnconserved.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
375 showunconserved_actionPerformed(e);
378 // / TODO: fit these in to preferences panel!!!!!
379 shareSelections.setFont(verdana11);
380 shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
381 shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
382 shareSelections.setSelected(true);
383 shareSelections.setText("Share selection across views");
384 followHighlight.setFont(verdana11);
385 followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
386 followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
387 // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
388 followHighlight.setSelected(true);
389 followHighlight.setText("Scroll to highlighted regions");
391 gapLabel.setFont(verdana11);
392 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
393 gapLabel.setText("Gap Symbol ");
394 colour.setFont(verdana11);
395 colour.setBounds(new Rectangle(172, 225, 155, 21));
396 colourLabel.setFont(verdana11);
397 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
398 colourLabel.setText("Colour ");
399 fontLabel.setFont(verdana11);
400 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
401 fontLabel.setText("Font ");
402 fontSizeCB.setFont(verdana11);
403 fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
404 fontStyleCB.setFont(verdana11);
405 fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
406 fontNameCB.setFont(verdana11);
407 fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
408 gapSymbolCB.setFont(verdana11);
409 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
410 startupCheckbox.setText("Open file");
411 startupCheckbox.setFont(verdana11);
412 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
413 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
414 startupCheckbox.setSelected(true);
415 startupFileTextfield.setFont(verdana11);
416 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
417 startupFileTextfield.addMouseListener(new MouseAdapter()
419 public void mouseClicked(MouseEvent e)
421 if (e.getClickCount() > 1)
423 startupFileTextfield_mouseClicked();
428 connectTab.setLayout(gridBagLayout3);
429 serverLabel.setText("Address");
430 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
431 serverLabel.setFont(verdana11);
432 proxyServerTB.setFont(verdana11);
433 proxyPortTB.setFont(verdana11);
434 portLabel.setFont(verdana11);
435 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
436 portLabel.setText("Port");
437 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
438 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
439 browserLabel.setText("Default Browser (Unix)");
440 defaultBrowser.setFont(verdana11);
441 defaultBrowser.setText("");
442 usagestats.setText("Send usage statistics");
443 usagestats.setFont(verdana11);
444 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
445 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
446 questionnaire.setText("Check for questionnaires");
447 questionnaire.setFont(verdana11);
448 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
449 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
450 versioncheck.setText("Check for latest version");
451 versioncheck.setFont(verdana11);
452 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
453 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
454 newLink.setText("New");
455 newLink.addActionListener(new java.awt.event.ActionListener()
457 public void actionPerformed(ActionEvent e)
459 newLink_actionPerformed(e);
462 editLink.setText("Edit");
463 editLink.addActionListener(new java.awt.event.ActionListener()
465 public void actionPerformed(ActionEvent e)
467 editLink_actionPerformed(e);
470 deleteLink.setText("Delete");
471 deleteLink.addActionListener(new java.awt.event.ActionListener()
473 public void actionPerformed(ActionEvent e)
475 deleteLink_actionPerformed(e);
479 linkURLList.addListSelectionListener(new ListSelectionListener()
481 public void valueChanged(ListSelectionEvent e)
483 int index = linkURLList.getSelectedIndex();
484 linkNameList.setSelectedIndex(index);
488 linkNameList.addListSelectionListener(new ListSelectionListener()
490 public void valueChanged(ListSelectionEvent e)
492 int index = linkNameList.getSelectedIndex();
493 linkURLList.setSelectedIndex(index);
497 linkScrollPane.setBorder(null);
498 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
499 linkPanel.setLayout(borderLayout2);
500 editLinkButtons.setLayout(gridLayout1);
501 gridLayout1.setRows(3);
502 linkNameList.setFont(verdana11);
503 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
504 linkPanel2.setLayout(borderLayout3);
505 linkURLList.setFont(verdana11);
506 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
508 defaultBrowser.addMouseListener(new MouseAdapter()
510 public void mouseClicked(MouseEvent e)
512 if (e.getClickCount() > 1)
514 defaultBrowser_mouseClicked(e);
518 useProxy.setFont(verdana11);
519 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
520 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
521 useProxy.setText("Use a proxy server");
522 useProxy.addActionListener(new ActionListener()
524 public void actionPerformed(ActionEvent e)
526 useProxy_actionPerformed();
529 jPanel1.setBorder(titledBorder1);
530 jPanel1.setLayout(gridBagLayout1);
531 sortby.setFont(verdana11);
532 sortby.setBounds(new Rectangle(172, 249, 155, 21));
533 sortLabel.setFont(verdana11);
534 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
535 sortLabel.setText("Sort by ");
536 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
537 jPanel2.setLayout(gridLayout2);
538 gridLayout2.setRows(13);
539 exportTab.setLayout(null);
540 epsLabel.setFont(verdana11);
541 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
542 epsLabel.setText("EPS Rendering Style");
543 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
544 epsRendering.setFont(verdana11);
545 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
546 jLabel1.setFont(verdana11);
547 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
548 jLabel1.setText("Append /start-end (/15-380)");
549 jLabel1.setFont(verdana11);
550 fastajv.setFont(verdana11);
551 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
552 clustaljv.setText("Clustal ");
553 blcjv.setText("BLC ");
554 fastajv.setText("Fasta ");
555 msfjv.setText("MSF ");
556 pfamjv.setText("PFAM ");
557 pileupjv.setText("Pileup ");
558 msfjv.setFont(verdana11);
559 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
560 pirjv.setText("PIR ");
561 jPanel11.setFont(verdana11);
562 jPanel11.setBorder(titledBorder2);
563 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
564 jPanel11.setLayout(gridLayout3);
565 blcjv.setFont(verdana11);
566 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
567 clustaljv.setFont(verdana11);
568 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
569 pfamjv.setFont(verdana11);
570 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
571 pileupjv.setFont(verdana11);
572 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
573 pirjv.setFont(verdana11);
574 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
575 seqLimit.setFont(verdana11);
576 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
577 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
578 seqLimit.setText("Full Sequence Id");
579 gridLayout3.setRows(8);
580 smoothFont.setFont(verdana11);
581 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
582 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
583 smoothFont.setText("Smooth Font");
584 calcTab.setLayout(null);
585 autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
587 autoCalculateConsCheck.setText("AutoCalculate Consensus");
588 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
589 padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
590 padGaps.setText("Pad gaps when editing");
591 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
592 modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
593 modellerOutput.setText("Use Modeller Output");
594 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
595 dasPanel.setLayout(borderLayout4);
596 wsPanel.setLayout(borderLayout5);
597 wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
598 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
599 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
600 wrap.setText("Wrap Alignment");
601 rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
602 rightAlign.setForeground(Color.black);
603 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
604 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
605 rightAlign.setText("Right Align Ids");
606 idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
607 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
608 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
609 idItalics.setText("Sequence Name Italics");
610 openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
611 openoverv.setActionCommand("Open Overview");
612 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
613 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
614 openoverv.setText("Open Overview");
615 jPanel2.add(fullScreen);
616 jPanel2.add(openoverv);
617 jPanel2.add(seqLimit);
618 jPanel2.add(rightAlign);
619 jPanel2.add(fontLabel);
620 jPanel2.add(showUnconserved);
621 jPanel2.add(idItalics);
622 jPanel2.add(smoothFont);
624 jPanel2.add(gapLabel);
625 jPanel2.add(colourLabel);
626 jPanel2.add(sortLabel);
627 jPanel2.add(startupCheckbox);
628 visualTab.add(annotations);
629 visualTab.add(startupFileTextfield);
630 visualTab.add(sortby);
631 visualTab.add(colour);
632 visualTab.add(gapSymbolCB);
633 visualTab.add(fontNameCB);
634 visualTab.add(fontSizeCB);
635 visualTab.add(fontStyleCB);
636 annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
637 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
638 annsettingsPanel.add(autoAnnotSettings1);
639 annsettingsPanel.add(autoAnnotSettings2);
640 annsettingsPanel.add(autoAnnotSettings3);
641 autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
642 autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
643 autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
644 visualTab.add(annsettingsPanel);
645 Border jb = new EmptyBorder(1, 1, 4, 5);
646 quality.setBorder(jb);
647 conservation.setBorder(jb);
648 identity.setBorder(jb);
649 showConsensbits.setBorder(jb);
650 showGroupbits.setBorder(jb);
651 showGroupConsensus.setBorder(jb);
652 showGroupConservation.setBorder(jb);
653 showConsensHistogram.setBorder(jb);
654 showConsensLogo.setBorder(jb);
656 autoAnnotSettings2.add(conservation);
657 autoAnnotSettings1.add(quality);
658 autoAnnotSettings3.add(identity);
659 autoAnnotSettings1.add(showGroupbits);
660 autoAnnotSettings3.add(showGroupConsensus);
661 autoAnnotSettings2.add(showGroupConservation);
662 autoAnnotSettings1.add(showConsensbits);
663 autoAnnotSettings2.add(showConsensHistogram);
664 autoAnnotSettings3.add(showConsensLogo);
666 JPanel tooltipSettings = new JPanel();
667 tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
668 tooltipSettings.setBounds(173, 130, 200, 62);
669 tooltipSettings.setLayout(new GridLayout(2, 1));
670 tooltipSettings.add(showDbRefTooltip);
671 tooltipSettings.add(showNpTooltip);
672 visualTab.add(tooltipSettings);
673 visualTab.add(jPanel2);
675 linkPanel.add(editLinkButtons, BorderLayout.EAST);
676 editLinkButtons.add(newLink, null);
677 editLinkButtons.add(editLink, null);
678 editLinkButtons.add(deleteLink, null);
679 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
680 linkScrollPane.getViewport().add(linkPanel2, null);
681 linkPanel2.add(linkURLList, BorderLayout.CENTER);
682 linkPanel2.add(linkNameList, BorderLayout.WEST);
683 okCancelPanel.add(ok);
684 okCancelPanel.add(cancel);
685 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
687 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
688 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
689 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
691 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
692 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
694 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
695 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
696 16, 0, 0, 12), 359, -17));
697 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
698 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
699 21, 0, 35, 12), 4, 6));
700 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
701 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
702 new Insets(16, 0, 0, 0), 5, 1));
703 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
704 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
705 new Insets(0, 2, 4, 2), 54, 1));
706 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
707 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
708 new Insets(0, 2, 4, 0), 263, 1));
709 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
710 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
711 new Insets(15, 0, 0, 15), 307, 1));
712 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
713 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
714 new Insets(0, 2, 4, 2), 70, 1));
715 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
716 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
717 new Insets(0, 2, 4, 2), 70, 1));
718 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
719 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
720 new Insets(0, 2, 4, 2), 70, 1));
722 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
723 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
725 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
726 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
727 gapSymbolCB.setRenderer(dlcr);
729 tabbedPane.add(visualTab, "Visual");
730 tabbedPane.add(connectTab, "Connections");
731 tabbedPane.add(exportTab, "Output");
732 jPanel11.add(jLabel1);
734 jPanel11.add(clustaljv);
735 jPanel11.add(fastajv);
737 jPanel11.add(pfamjv);
738 jPanel11.add(pileupjv);
740 exportTab.add(modellerOutput);
741 tabbedPane.add(calcTab, "Editing");
742 calcTab.add(autoCalculateConsCheck);
743 calcTab.add(padGaps);
744 tabbedPane.add(dasPanel, "DAS Settings");
745 tabbedPane.add(wsPanel, "Web Services");
747 exportTab.add(epsLabel);
748 exportTab.add(epsRendering);
749 exportTab.add(jPanel11);
752 protected void showunconserved_actionPerformed(ActionEvent e)
754 // TODO Auto-generated method stub
764 public void ok_actionPerformed(ActionEvent e)
774 public void cancel_actionPerformed(ActionEvent e)
784 public void annotations_actionPerformed(ActionEvent e)
791 public void startupFileTextfield_mouseClicked()
795 public void newLink_actionPerformed(ActionEvent e)
800 public void editLink_actionPerformed(ActionEvent e)
805 public void deleteLink_actionPerformed(ActionEvent e)
810 public void defaultBrowser_mouseClicked(MouseEvent e)
815 public void linkURLList_keyTyped(KeyEvent e)
820 public void useProxy_actionPerformed()
822 proxyServerTB.setEnabled(useProxy.isSelected());
823 proxyPortTB.setEnabled(useProxy.isSelected());