2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 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;
20 import jalview.gui.JvSwingUtils;
23 import java.awt.event.*;
26 import javax.swing.border.*;
27 import javax.swing.event.*;
28 import java.awt.Rectangle;
36 public class GPreferences extends JPanel
38 JTabbedPane tabbedPane = new JTabbedPane();
40 JButton ok = new JButton();
42 JButton cancel = new JButton();
44 JPanel okCancelPanel = new JPanel();
46 BorderLayout borderLayout1 = new BorderLayout();
48 protected JCheckBox quality = new JCheckBox();
50 JPanel visualTab = new JPanel();
51 JPanel visual2Tab = new JPanel();
53 protected JCheckBox fullScreen = new JCheckBox();
55 protected JCheckBox conservation = new JCheckBox();
57 protected JCheckBox identity = new JCheckBox();
59 protected JCheckBox annotations = new JCheckBox();
61 protected JPanel minColour = new JPanel();
62 JLabel mincolourLabel = new JLabel();
64 protected JPanel maxColour = new JPanel();
65 JLabel maxcolourLabel = new JLabel();
67 JLabel gapLabel = new JLabel();
69 protected JComboBox colour = new JComboBox();
71 JLabel colourLabel = new JLabel();
73 JLabel fontLabel = new JLabel();
75 protected JComboBox fontSizeCB = new JComboBox();
77 protected JComboBox fontStyleCB = new JComboBox();
79 protected JComboBox fontNameCB = new JComboBox();
81 protected JComboBox gapSymbolCB = new JComboBox();
83 protected JCheckBox startupCheckbox = new JCheckBox();
85 protected JTextField startupFileTextfield = new JTextField();
87 JPanel connectTab = new JPanel();
89 JLabel serverLabel = new JLabel();
91 protected JList linkURLList = new JList();
93 protected JTextField proxyServerTB = new JTextField();
95 protected JTextField proxyPortTB = new JTextField();
97 JLabel portLabel = new JLabel();
99 JLabel browserLabel = new JLabel();
101 protected JTextField defaultBrowser = new JTextField();
103 JButton newLink = new JButton();
105 JButton editLink = new JButton();
107 JButton deleteLink = new JButton();
109 JScrollPane linkScrollPane = new JScrollPane();
111 JPanel linkPanel = new JPanel();
113 BorderLayout borderLayout2 = new BorderLayout();
115 JPanel editLinkButtons = new JPanel();
117 GridLayout gridLayout1 = new GridLayout();
119 protected JList linkNameList = new JList();
121 JPanel linkPanel2 = new JPanel();
123 BorderLayout borderLayout3 = new BorderLayout();
125 protected JCheckBox useProxy = new JCheckBox();
127 JPanel jPanel1 = new JPanel();
129 TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
131 TitledBorder titledBorder2 = new TitledBorder("File Output");
133 GridBagLayout gridBagLayout2 = new GridBagLayout();
135 GridBagLayout gridBagLayout1 = new GridBagLayout();
137 GridBagLayout gridBagLayout3 = new GridBagLayout();
139 protected JComboBox sortby = new JComboBox();
141 JLabel sortLabel = new JLabel();
143 JPanel jPanel2 = new JPanel();
144 JPanel visual2panel = new JPanel();
146 GridLayout gridLayout2 = new GridLayout();
148 GridLayout gridLayout4 = new GridLayout();
150 JPanel annsettingsPanel = new JPanel();
152 JPanel autoAnnotSettings1 = new JPanel();
154 JPanel autoAnnotSettings2 = new JPanel();
156 JPanel autoAnnotSettings3 = new JPanel();
158 JPanel exportTab = new JPanel();
160 JLabel epsLabel = new JLabel();
162 protected JComboBox epsRendering = new JComboBox();
164 protected JLabel userIdWidthlabel = new JLabel();
165 protected JCheckBox autoIdWidth = new JCheckBox();
166 protected JTextField userIdWidth = new JTextField();
169 JLabel jLabel1 = new JLabel();
171 protected JCheckBox blcjv = new JCheckBox();
173 protected JCheckBox pileupjv = new JCheckBox();
175 protected JCheckBox clustaljv = new JCheckBox();
177 protected JCheckBox msfjv = new JCheckBox();
179 protected JCheckBox fastajv = new JCheckBox();
181 protected JCheckBox pfamjv = new JCheckBox();
183 FlowLayout flowLayout1 = new FlowLayout();
185 protected JCheckBox pirjv = new JCheckBox();
187 JPanel jPanel11 = new JPanel();
189 Font verdana11 = JvSwingUtils.getLabelFont();
191 protected JCheckBox seqLimit = new JCheckBox();
193 GridLayout gridLayout3 = new GridLayout();
195 protected JCheckBox smoothFont = new JCheckBox();
197 JPanel calcTab = new JPanel();
199 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
201 protected JCheckBox padGaps = new JCheckBox();
203 protected JCheckBox modellerOutput = new JCheckBox();
205 protected JPanel dasPanel = new JPanel();
207 BorderLayout borderLayout4 = new BorderLayout();
209 protected JPanel wsPanel = new JPanel();
211 BorderLayout borderLayout5 = new BorderLayout();
213 protected JCheckBox wrap = new JCheckBox();
215 protected JCheckBox rightAlign = new JCheckBox();
217 protected JCheckBox showUnconserved = new JCheckBox();
219 protected JCheckBox showDbRefTooltip = new JCheckBox();
221 protected JCheckBox showNpTooltip = new JCheckBox();
223 protected JCheckBox idItalics = new JCheckBox();
225 protected JCheckBox openoverv = new JCheckBox();
227 protected JCheckBox usagestats = new JCheckBox();
229 protected JCheckBox questionnaire = new JCheckBox();
231 protected JCheckBox versioncheck = new JCheckBox();
233 protected JLabel showGroupbits = new JLabel();
235 protected JLabel showConsensbits = new JLabel();
237 protected JCheckBox showConsensLogo = new JCheckBox();
239 protected JCheckBox showConsensHistogram = new JCheckBox();
241 protected JCheckBox showGroupConsensus = new JCheckBox();
243 protected JCheckBox showGroupConservation = new JCheckBox();
245 protected JCheckBox shareSelections = new JCheckBox();
247 protected JCheckBox followHighlight = new JCheckBox();
249 protected JCheckBox sortByTree= new JCheckBox();
252 * Creates a new GPreferences object.
254 public GPreferences()
259 } catch (Exception ex)
261 ex.printStackTrace();
271 private void jbInit() throws Exception
273 this.setLayout(borderLayout1);
275 ok.addActionListener(new ActionListener()
277 public void actionPerformed(ActionEvent e)
279 ok_actionPerformed(e);
282 cancel.setText("Cancel");
283 cancel.addActionListener(new ActionListener()
285 public void actionPerformed(ActionEvent e)
287 cancel_actionPerformed(e);
290 quality.setEnabled(false);
291 quality.setFont(verdana11);
292 quality.setHorizontalAlignment(SwingConstants.RIGHT);
293 quality.setHorizontalTextPosition(SwingConstants.LEFT);
294 quality.setSelected(true);
295 quality.setText("Quality");
296 visualTab.setBorder(new TitledBorder("Open new alignment"));
297 visualTab.setLayout(null);
298 visual2Tab.setBorder(new TitledBorder("Open new alignment"));
299 visual2Tab.setLayout(new FlowLayout());
300 fullScreen.setFont(verdana11);
301 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
302 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
303 fullScreen.setText("Maximise Window");
304 conservation.setEnabled(false);
305 conservation.setFont(verdana11);
306 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
307 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
308 conservation.setSelected(true);
309 conservation.setText("Conservation");
310 identity.setEnabled(false);
311 identity.setFont(verdana11);
312 identity.setHorizontalAlignment(SwingConstants.RIGHT);
313 identity.setHorizontalTextPosition(SwingConstants.LEFT);
314 identity.setSelected(true);
315 identity.setText("Consensus");
316 showGroupbits.setFont(verdana11);
317 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
318 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
319 showGroupbits.setText("Show group:");
320 showConsensbits.setFont(verdana11);
321 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
322 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
323 showConsensbits.setText("Consensus:");
324 showConsensHistogram.setEnabled(false);
325 showConsensHistogram.setFont(verdana11);
326 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
327 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
328 showConsensHistogram.setSelected(true);
329 showConsensHistogram.setText("Histogram");
330 showConsensLogo.setEnabled(false);
331 showConsensLogo.setFont(verdana11);
332 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
333 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
334 showConsensLogo.setSelected(true);
335 showConsensLogo.setText("Logo");
336 showGroupConsensus.setEnabled(false);
337 showGroupConsensus.setFont(verdana11);
338 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
339 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
340 showGroupConsensus.setSelected(true);
341 showGroupConsensus.setText("Consensus");
342 showGroupConservation.setEnabled(false);
343 showGroupConservation.setFont(verdana11);
344 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
345 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
346 showGroupConservation.setSelected(true);
347 showGroupConservation.setText("Conservation");
348 showNpTooltip.setEnabled(true);
349 showNpTooltip.setFont(verdana11);
350 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
351 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
352 showNpTooltip.setSelected(true);
353 showNpTooltip.setText("Non-positional Features");
354 showDbRefTooltip.setEnabled(true);
355 showDbRefTooltip.setFont(verdana11);
356 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
357 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
358 showDbRefTooltip.setSelected(true);
359 showDbRefTooltip.setText("Database References");
360 annotations.setFont(verdana11);
361 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
362 annotations.setHorizontalTextPosition(SwingConstants.LEADING);
363 annotations.setSelected(true);
364 annotations.setText("Show Annotations");
365 annotations.setBounds(new Rectangle(169, 12, 200, 23));
366 annotations.addActionListener(new ActionListener()
368 public void actionPerformed(ActionEvent e)
370 annotations_actionPerformed(e);
373 identity.addActionListener(new ActionListener()
375 public void actionPerformed(ActionEvent e)
377 annotations_actionPerformed(e);
380 showGroupConsensus.addActionListener(new ActionListener()
382 public void actionPerformed(ActionEvent e)
384 annotations_actionPerformed(e);
387 showUnconserved.setFont(verdana11);
388 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
389 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
390 showUnconserved.setSelected(true);
391 showUnconserved.setText("Show Unconserved");
392 showUnconserved.addActionListener(new ActionListener()
394 public void actionPerformed(ActionEvent e)
396 showunconserved_actionPerformed(e);
399 // / TODO: fit these in to preferences panel!!!!!
400 shareSelections.setFont(verdana11);
401 shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
402 shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
403 shareSelections.setSelected(true);
404 shareSelections.setText("Share selection across views");
405 followHighlight.setFont(verdana11);
406 followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
407 followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
408 // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
409 followHighlight.setSelected(true);
410 followHighlight.setText("Scroll to highlighted regions");
412 gapLabel.setFont(verdana11);
413 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
414 gapLabel.setText("Gap Symbol ");
415 colour.setFont(verdana11);
416 colour.setBounds(new Rectangle(172, 225, 155, 21));
417 colourLabel.setFont(verdana11);
418 colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
419 colourLabel.setText("Alignment Colour ");
420 fontLabel.setFont(verdana11);
421 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
422 fontLabel.setText("Font ");
423 fontSizeCB.setFont(verdana11);
424 fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
425 fontStyleCB.setFont(verdana11);
426 fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
427 fontNameCB.setFont(verdana11);
428 fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
429 gapSymbolCB.setFont(verdana11);
430 gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
431 mincolourLabel.setFont(verdana11);
432 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
433 mincolourLabel.setText("Minimum Colour");
434 minColour.setFont(verdana11);
435 minColour.setBorder(BorderFactory.createEtchedBorder());
436 minColour.setPreferredSize(new Dimension(40, 20));
437 minColour.addMouseListener(new MouseAdapter()
439 public void mousePressed(MouseEvent e)
441 minColour_actionPerformed();
444 maxcolourLabel.setFont(verdana11);
445 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
446 maxcolourLabel.setText("Maximum Colour ");
447 maxColour.setFont(verdana11);
448 maxColour.setBorder(BorderFactory.createEtchedBorder());
449 maxColour.setPreferredSize(new Dimension(40, 20));
450 maxColour.addMouseListener(new MouseAdapter()
452 public void mousePressed(MouseEvent e)
454 maxColour_actionPerformed();
458 startupCheckbox.setText("Open file");
459 startupCheckbox.setFont(verdana11);
460 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
461 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
462 startupCheckbox.setSelected(true);
463 startupFileTextfield.setFont(verdana11);
464 startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
465 startupFileTextfield.addMouseListener(new MouseAdapter()
467 public void mouseClicked(MouseEvent e)
469 if (e.getClickCount() > 1)
471 startupFileTextfield_mouseClicked();
476 connectTab.setLayout(gridBagLayout3);
477 serverLabel.setText("Address");
478 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
479 serverLabel.setFont(verdana11);
480 proxyServerTB.setFont(verdana11);
481 proxyPortTB.setFont(verdana11);
482 portLabel.setFont(verdana11);
483 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
484 portLabel.setText("Port");
485 browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
486 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
487 browserLabel.setText("Default Browser (Unix)");
488 defaultBrowser.setFont(verdana11);
489 defaultBrowser.setText("");
490 usagestats.setText("Send usage statistics");
491 usagestats.setFont(verdana11);
492 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
493 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
494 questionnaire.setText("Check for questionnaires");
495 questionnaire.setFont(verdana11);
496 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
497 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
498 versioncheck.setText("Check for latest version");
499 versioncheck.setFont(verdana11);
500 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
501 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
502 newLink.setText("New");
503 newLink.addActionListener(new java.awt.event.ActionListener()
505 public void actionPerformed(ActionEvent e)
507 newLink_actionPerformed(e);
510 editLink.setText("Edit");
511 editLink.addActionListener(new java.awt.event.ActionListener()
513 public void actionPerformed(ActionEvent e)
515 editLink_actionPerformed(e);
518 deleteLink.setText("Delete");
519 deleteLink.addActionListener(new java.awt.event.ActionListener()
521 public void actionPerformed(ActionEvent e)
523 deleteLink_actionPerformed(e);
527 linkURLList.addListSelectionListener(new ListSelectionListener()
529 public void valueChanged(ListSelectionEvent e)
531 int index = linkURLList.getSelectedIndex();
532 linkNameList.setSelectedIndex(index);
536 linkNameList.addListSelectionListener(new ListSelectionListener()
538 public void valueChanged(ListSelectionEvent e)
540 int index = linkNameList.getSelectedIndex();
541 linkURLList.setSelectedIndex(index);
545 linkScrollPane.setBorder(null);
546 linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
547 linkPanel.setLayout(borderLayout2);
548 editLinkButtons.setLayout(gridLayout1);
549 gridLayout1.setRows(3);
550 linkNameList.setFont(verdana11);
551 linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
552 linkPanel2.setLayout(borderLayout3);
553 linkURLList.setFont(verdana11);
554 linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
556 defaultBrowser.addMouseListener(new MouseAdapter()
558 public void mouseClicked(MouseEvent e)
560 if (e.getClickCount() > 1)
562 defaultBrowser_mouseClicked(e);
566 useProxy.setFont(verdana11);
567 useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
568 useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
569 useProxy.setText("Use a proxy server");
570 useProxy.addActionListener(new ActionListener()
572 public void actionPerformed(ActionEvent e)
574 useProxy_actionPerformed();
577 jPanel1.setBorder(titledBorder1);
578 jPanel1.setLayout(gridBagLayout1);
579 sortby.setFont(verdana11);
580 sortby.setBounds(new Rectangle(172, 249, 155, 21));
581 sortLabel.setFont(verdana11);
582 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
583 sortLabel.setText("Sort by ");
584 jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
585 jPanel2.setLayout(gridLayout2);
586 gridLayout2.setRows(12);
587 exportTab.setLayout(null);
588 epsLabel.setFont(verdana11);
589 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
590 epsLabel.setText("EPS Rendering Style");
591 epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
592 epsRendering.setFont(verdana11);
593 epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
594 jLabel1.setFont(verdana11);
595 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
596 jLabel1.setText("Append /start-end (/15-380)");
597 jLabel1.setFont(verdana11);
598 fastajv.setFont(verdana11);
599 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
600 clustaljv.setText("Clustal ");
601 blcjv.setText("BLC ");
602 fastajv.setText("Fasta ");
603 msfjv.setText("MSF ");
604 pfamjv.setText("PFAM ");
605 pileupjv.setText("Pileup ");
606 msfjv.setFont(verdana11);
607 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
608 pirjv.setText("PIR ");
609 jPanel11.setFont(verdana11);
610 jPanel11.setBorder(titledBorder2);
611 jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
612 jPanel11.setLayout(gridLayout3);
613 blcjv.setFont(verdana11);
614 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
615 clustaljv.setFont(verdana11);
616 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
617 pfamjv.setFont(verdana11);
618 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
619 pileupjv.setFont(verdana11);
620 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
621 pirjv.setFont(verdana11);
622 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
623 seqLimit.setFont(verdana11);
624 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
625 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
626 seqLimit.setText("Full Sequence Id");
627 gridLayout3.setRows(8);
628 smoothFont.setFont(verdana11);
629 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
630 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
631 smoothFont.setText("Smooth Font");
632 calcTab.setLayout(null);
633 autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
634 autoCalculateConsCheck.setText("AutoCalculate Consensus");
635 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
636 padGaps.setFont(JvSwingUtils.getLabelFont());
637 padGaps.setText("Pad Gaps When Editing");
638 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
639 sortByTree.setFont(JvSwingUtils.getLabelFont());
640 sortByTree.setText("Sort With New Tree");
641 sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
642 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
644 autoIdWidth.setFont(JvSwingUtils.getLabelFont());
645 autoIdWidth.setText("Autofit Figure ID width");
646 autoIdWidth.setBounds(new Rectangle(228, 96,188,23));
647 autoIdWidth.addActionListener(new ActionListener()
651 public void actionPerformed(ActionEvent e)
653 autoIdWidth_actionPerformed();
656 userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
657 userIdWidthlabel.setText("Figure ID column width");
658 userIdWidthlabel.setBounds(new Rectangle(236, 120,168,23));
659 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
660 userIdWidth.setText("");
661 userIdWidth.setBounds(new Rectangle(232,144,84,23));
662 userIdWidth.addActionListener(new ActionListener()
666 public void actionPerformed(ActionEvent e)
668 userIdWidth_actionPerformed();
671 modellerOutput.setFont(JvSwingUtils.getLabelFont());
672 modellerOutput.setText("Use Modeller Output");
673 modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
675 dasPanel.setLayout(borderLayout4);
676 wsPanel.setLayout(borderLayout5);
677 wrap.setFont(JvSwingUtils.getLabelFont());
678 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
679 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
680 wrap.setText("Wrap Alignment");
681 rightAlign.setFont(JvSwingUtils.getLabelFont());
682 rightAlign.setForeground(Color.black);
683 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
684 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
685 rightAlign.setText("Right Align Ids");
686 idItalics.setFont(JvSwingUtils.getLabelFont());
687 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
688 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
689 idItalics.setText("Sequence Name Italics");
690 openoverv.setFont(JvSwingUtils.getLabelFont());
691 openoverv.setActionCommand("Open Overview");
692 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
693 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
694 openoverv.setText("Open Overview");
695 jPanel2.add(fullScreen);
696 jPanel2.add(openoverv);
697 jPanel2.add(seqLimit);
698 jPanel2.add(rightAlign);
699 jPanel2.add(fontLabel);
700 jPanel2.add(showUnconserved);
701 jPanel2.add(idItalics);
702 jPanel2.add(smoothFont);
703 jPanel2.add(gapLabel);
705 jPanel2.add(sortLabel);
706 jPanel2.add(startupCheckbox);
707 visualTab.add(annotations);
708 visualTab.add(startupFileTextfield);
709 visualTab.add(sortby);
710 visualTab.add(gapSymbolCB);
711 visualTab.add(fontNameCB);
712 visualTab.add(fontSizeCB);
713 visualTab.add(fontStyleCB);
714 annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
715 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
716 annsettingsPanel.add(autoAnnotSettings1);
717 annsettingsPanel.add(autoAnnotSettings2);
718 annsettingsPanel.add(autoAnnotSettings3);
719 autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
720 autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
721 autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
722 visualTab.add(annsettingsPanel);
723 Border jb = new EmptyBorder(1, 1, 4, 5);
724 quality.setBorder(jb);
725 conservation.setBorder(jb);
726 identity.setBorder(jb);
727 showConsensbits.setBorder(jb);
728 showGroupbits.setBorder(jb);
729 showGroupConsensus.setBorder(jb);
730 showGroupConservation.setBorder(jb);
731 showConsensHistogram.setBorder(jb);
732 showConsensLogo.setBorder(jb);
734 autoAnnotSettings2.add(conservation);
735 autoAnnotSettings1.add(quality);
736 autoAnnotSettings3.add(identity);
737 autoAnnotSettings1.add(showGroupbits);
738 autoAnnotSettings3.add(showGroupConsensus);
739 autoAnnotSettings2.add(showGroupConservation);
740 autoAnnotSettings1.add(showConsensbits);
741 autoAnnotSettings2.add(showConsensHistogram);
742 autoAnnotSettings3.add(showConsensLogo);
744 JPanel tooltipSettings = new JPanel();
745 tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
746 tooltipSettings.setBounds(173, 130, 200, 62);
747 tooltipSettings.setLayout(new GridLayout(2, 1));
748 tooltipSettings.add(showDbRefTooltip);
749 tooltipSettings.add(showNpTooltip);
750 visualTab.add(tooltipSettings);
751 visualTab.add(jPanel2);
752 JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
753 JPanel annotationShding=new JPanel();
754 annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
755 annotationShding.setLayout(new GridLayout(1,2));
756 JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
757 JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
758 visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
760 // visual2panel.add(minColour);
761 // visual2panel.add(maxColour);
762 // visual2Tab.add(visual2panel);
764 linkPanel.add(editLinkButtons, BorderLayout.EAST);
765 editLinkButtons.add(newLink, null);
766 editLinkButtons.add(editLink, null);
767 editLinkButtons.add(deleteLink, null);
768 linkPanel.add(linkScrollPane, BorderLayout.CENTER);
769 linkScrollPane.getViewport().add(linkPanel2, null);
770 linkPanel2.add(linkURLList, BorderLayout.CENTER);
771 linkPanel2.add(linkNameList, BorderLayout.WEST);
772 okCancelPanel.add(ok);
773 okCancelPanel.add(cancel);
774 this.add(tabbedPane, java.awt.BorderLayout.CENTER);
776 this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
777 jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
778 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
780 jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
781 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
783 connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
784 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
785 16, 0, 0, 12), 359, -17));
786 connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
787 GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
788 21, 0, 35, 12), 4, 6));
789 connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
790 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
791 new Insets(16, 0, 0, 0), 5, 1));
792 jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
793 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
794 new Insets(0, 2, 4, 2), 54, 1));
795 jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
796 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
797 new Insets(0, 2, 4, 0), 263, 1));
798 connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
799 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
800 new Insets(15, 0, 0, 15), 307, 1));
801 connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
802 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
803 new Insets(0, 2, 4, 2), 70, 1));
804 connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
805 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
806 new Insets(0, 2, 4, 2), 70, 1));
807 connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
808 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
809 new Insets(0, 2, 4, 2), 70, 1));
811 jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
812 GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
814 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
815 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
816 gapSymbolCB.setRenderer(dlcr);
818 tabbedPane.add(visualTab, "Visual");
819 tabbedPane.add(visual2Tab,"Colours");
820 tabbedPane.add(connectTab, "Connections");
821 tabbedPane.add(exportTab, "Output");
822 jPanel11.add(jLabel1);
824 jPanel11.add(clustaljv);
825 jPanel11.add(fastajv);
827 jPanel11.add(pfamjv);
828 jPanel11.add(pileupjv);
830 exportTab.add(autoIdWidth);
831 exportTab.add(userIdWidth);
832 exportTab.add(userIdWidthlabel);
833 exportTab.add(modellerOutput);
834 tabbedPane.add(calcTab, "Editing");
835 calcTab.add(autoCalculateConsCheck);
836 calcTab.add(padGaps);
837 calcTab.add(sortByTree);
839 tabbedPane.add(dasPanel, "DAS Settings");
840 tabbedPane.add(wsPanel, "Web Services");
842 exportTab.add(epsLabel);
843 exportTab.add(epsRendering);
844 exportTab.add(jPanel11);
847 protected void autoIdWidth_actionPerformed()
849 // TODO Auto-generated method stub
853 protected void userIdWidth_actionPerformed()
855 // TODO Auto-generated method stub
859 protected void maxColour_actionPerformed()
861 // TODO Auto-generated method stub
865 protected void minColour_actionPerformed()
867 // TODO Auto-generated method stub
871 protected void showunconserved_actionPerformed(ActionEvent e)
873 // TODO Auto-generated method stub
883 public void ok_actionPerformed(ActionEvent e)
893 public void cancel_actionPerformed(ActionEvent e)
903 public void annotations_actionPerformed(ActionEvent e)
910 public void startupFileTextfield_mouseClicked()
914 public void newLink_actionPerformed(ActionEvent e)
919 public void editLink_actionPerformed(ActionEvent e)
924 public void deleteLink_actionPerformed(ActionEvent e)
929 public void defaultBrowser_mouseClicked(MouseEvent e)
934 public void linkURLList_keyTyped(KeyEvent e)
939 public void useProxy_actionPerformed()
941 proxyServerTB.setEnabled(useProxy.isSelected());
942 proxyPortTB.setEnabled(useProxy.isSelected());