2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Component;
26 import java.awt.Dimension;
27 import java.awt.FlowLayout;
29 import java.awt.GridBagConstraints;
30 import java.awt.GridBagLayout;
31 import java.awt.GridLayout;
32 import java.awt.Insets;
33 import java.awt.Rectangle;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.FocusEvent;
37 import java.awt.event.KeyEvent;
38 import java.awt.event.KeyListener;
39 import java.awt.event.MouseAdapter;
40 import java.awt.event.MouseEvent;
41 import java.util.Arrays;
42 import java.util.List;
44 import javax.swing.AbstractCellEditor;
45 import javax.swing.BorderFactory;
46 import javax.swing.ButtonGroup;
47 import javax.swing.DefaultListCellRenderer;
48 import javax.swing.JButton;
49 import javax.swing.JCheckBox;
50 import javax.swing.JComboBox;
51 import javax.swing.JFileChooser;
52 import javax.swing.JLabel;
53 import javax.swing.JPanel;
54 import javax.swing.JPasswordField;
55 import javax.swing.JRadioButton;
56 import javax.swing.JScrollPane;
57 import javax.swing.JSpinner;
58 import javax.swing.JTabbedPane;
59 import javax.swing.JTable;
60 import javax.swing.JTextArea;
61 import javax.swing.JTextField;
62 import javax.swing.ListSelectionModel;
63 import javax.swing.SpinnerModel;
64 import javax.swing.SpinnerNumberModel;
65 import javax.swing.SwingConstants;
66 import javax.swing.border.Border;
67 import javax.swing.border.EmptyBorder;
68 import javax.swing.border.EtchedBorder;
69 import javax.swing.border.TitledBorder;
70 import javax.swing.event.ChangeEvent;
71 import javax.swing.event.ChangeListener;
72 import javax.swing.event.DocumentEvent;
73 import javax.swing.event.DocumentListener;
74 import javax.swing.table.TableCellEditor;
75 import javax.swing.table.TableCellRenderer;
77 import jalview.bin.Cache;
78 import jalview.fts.core.FTSDataColumnPreferences;
79 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
80 import jalview.fts.service.pdb.PDBFTSRestClient;
81 import jalview.gui.Desktop;
82 import jalview.gui.JalviewBooleanRadioButtons;
83 import jalview.gui.JvOptionPane;
84 import jalview.gui.JvSwingUtils;
85 import jalview.gui.StructureViewer.ViewerType;
86 import jalview.io.BackupFilenameParts;
87 import jalview.io.BackupFiles;
88 import jalview.io.BackupFilesPresetEntry;
89 import jalview.io.IntKeyStringValueEntry;
90 import jalview.util.MessageManager;
91 import jalview.util.Platform;
94 * Base class for the Preferences panel.
99 public class GPreferences extends JPanel
101 private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
103 private static final Font LABEL_FONT_ITALIC = JvSwingUtils
104 .getLabelFont(false, true);
106 private static final Font LABEL_FONT_BOLD = JvSwingUtils
107 .getLabelFont(true, false);
110 * Visual tab components
112 protected JCheckBox fullScreen = new JCheckBox();
114 protected JCheckBox openoverv = new JCheckBox();
116 protected JCheckBox seqLimit = new JCheckBox();
118 protected JCheckBox rightAlign = new JCheckBox();
120 protected JComboBox<String> fontSizeCB = new JComboBox<>();
122 protected JComboBox<String> fontStyleCB = new JComboBox<>();
124 protected JComboBox<String> fontNameCB = new JComboBox<>();
126 protected JCheckBox showOccupancy = new JCheckBox();
128 protected JCheckBox showUnconserved = new JCheckBox();
130 protected JCheckBox idItalics = new JCheckBox();
132 protected JCheckBox smoothFont = new JCheckBox();
134 protected JCheckBox scaleProteinToCdna = new JCheckBox();
136 protected JComboBox<String> gapSymbolCB = new JComboBox<>();
138 protected JCheckBox wrap = new JCheckBox();
140 protected JComboBox<String> sortby = new JComboBox<>();
142 protected JComboBox<String> sortAnnBy = new JComboBox<>();
144 protected JComboBox<String> sortAutocalc = new JComboBox<>();
146 protected JCheckBox startupCheckbox = new JCheckBox();
148 protected JTextField startupFileTextfield = new JTextField();
150 // below are in the 'second column'
151 protected JCheckBox annotations = new JCheckBox();
153 protected JCheckBox quality = new JCheckBox();
155 protected JCheckBox conservation = new JCheckBox();
157 protected JCheckBox identity = new JCheckBox();
159 protected JCheckBox showGroupConsensus = new JCheckBox();
161 protected JCheckBox showGroupConservation = new JCheckBox();
163 protected JCheckBox showConsensHistogram = new JCheckBox();
165 protected JCheckBox showConsensLogo = new JCheckBox();
167 protected JCheckBox showDbRefTooltip = new JCheckBox();
169 protected JCheckBox showNpTooltip = new JCheckBox();
172 * Structure tab and components
174 protected JPanel structureTab;
176 protected JCheckBox structFromPdb = new JCheckBox();
178 protected JCheckBox useRnaView = new JCheckBox();
180 protected JCheckBox addSecondaryStructure = new JCheckBox();
182 protected JCheckBox addTempFactor = new JCheckBox();
184 protected JComboBox<String> structViewer = new JComboBox<>();
186 protected JLabel structureViewerPathLabel;
188 protected JTextField structureViewerPath = new JTextField();
190 protected ButtonGroup mappingMethod = new ButtonGroup();
192 protected JRadioButton siftsMapping = new JRadioButton();
194 protected JRadioButton nwMapping = new JRadioButton();
197 * Colours tab components
199 protected JPanel minColour = new JPanel();
201 protected JPanel maxColour = new JPanel();
203 protected JComboBox<String> protColour = new JComboBox<>();
205 protected JComboBox<String> nucColour = new JComboBox<>();
208 * Overview tab components
210 protected JPanel gapColour = new JPanel();
212 protected JPanel hiddenColour = new JPanel();
214 protected JCheckBox useLegacyGap;
216 protected JCheckBox showHiddenAtStart;
218 protected JLabel gapLabel;
221 * Connections tab components
223 protected JPanel connectTab;
225 protected JTable linkUrlTable = new JTable();
227 protected JButton editLink = new JButton();
229 protected JButton deleteLink = new JButton();
231 protected JTextField filterTB = new JTextField();
233 protected JButton doReset = new JButton();
235 protected JButton userOnly = new JButton();
237 protected JLabel httpLabel = new JLabel();
239 protected JLabel httpsLabel = new JLabel();
241 protected JLabel portLabel = new JLabel();
243 protected JLabel serverLabel = new JLabel();
245 protected JLabel portLabel2 = new JLabel();
247 protected JLabel serverLabel2 = new JLabel();
249 protected JLabel proxyAuthUsernameLabel = new JLabel();
251 protected JLabel proxyAuthPasswordLabel = new JLabel();
253 protected JLabel passwordNotStoredLabel = new JLabel();
255 protected JTextField proxyServerHttpTB = new JTextField();
257 protected JTextField proxyPortHttpTB = new JTextField();
259 protected JTextField proxyServerHttpsTB = new JTextField();
261 protected JTextField proxyPortHttpsTB = new JTextField();
263 protected JCheckBox proxyAuth = new JCheckBox();
265 protected JTextField proxyAuthUsernameTB = new JTextField();
267 protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
269 protected JTextField defaultBrowser = new JTextField();
271 protected ButtonGroup proxyType = new ButtonGroup();
273 protected JRadioButton noProxy = new JRadioButton();
275 protected JRadioButton systemProxy = new JRadioButton();
277 protected JRadioButton customProxy = new JRadioButton();
279 protected JButton applyProxyButton = new JButton();
281 protected JCheckBox usagestats = new JCheckBox();
283 protected JCheckBox questionnaire = new JCheckBox();
285 protected JCheckBox versioncheck = new JCheckBox();
288 * Output tab components
290 protected JComboBox<Object> epsRendering = new JComboBox<>();
292 protected JComboBox<Object> htmlRendering = new JComboBox<>();
294 protected JComboBox<Object> svgRendering = new JComboBox<>();
296 protected JLabel userIdWidthlabel = new JLabel();
298 protected JCheckBox autoIdWidth = new JCheckBox();
300 protected JTextField userIdWidth = new JTextField();
302 protected JCheckBox blcjv = new JCheckBox();
304 protected JCheckBox pileupjv = new JCheckBox();
306 protected JCheckBox clustaljv = new JCheckBox();
308 protected JCheckBox msfjv = new JCheckBox();
310 protected JCheckBox fastajv = new JCheckBox();
312 protected JCheckBox pfamjv = new JCheckBox();
314 protected JCheckBox pirjv = new JCheckBox();
316 protected JCheckBox modellerOutput = new JCheckBox();
318 protected JCheckBox embbedBioJSON = new JCheckBox();
321 * Editing tab components
323 protected JCheckBox autoCalculateConsCheck = new JCheckBox();
325 protected JCheckBox padGaps = new JCheckBox();
327 protected JCheckBox sortByTree = new JCheckBox();
332 protected JPanel wsTab = new JPanel();
335 * Backups tab components
336 * a lot of these are member variables instead of local variables only so that they
337 * can be enabled/disabled easily in one go
340 protected JCheckBox enableBackupFiles = new JCheckBox();
342 protected JPanel presetsPanel = new JPanel();
344 protected JLabel presetsComboLabel = new JLabel();
346 protected JCheckBox customiseCheckbox = new JCheckBox();
348 protected JButton revertButton = new JButton();
350 protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
352 private int backupfilesPresetsComboLastSelected = 0;
354 protected JPanel suffixPanel = new JPanel();
356 protected JPanel keepfilesPanel = new JPanel();
358 protected JPanel exampleFilesPanel = new JPanel();
360 protected JTextField suffixTemplate = new JTextField(null, 8);
362 protected JLabel suffixTemplateLabel = new JLabel();
364 protected JLabel suffixDigitsLabel = new JLabel();
366 protected JSpinner suffixDigitsSpinner = new JSpinner();
368 protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
370 protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
372 public JSpinner backupfilesRollMaxSpinner = new JSpinner();
374 protected JLabel oldBackupFilesLabel = new JLabel();
376 protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
378 protected JTextArea backupfilesExampleLabel = new JTextArea();
380 private final JTabbedPane tabbedPane = new JTabbedPane();
382 private JLabel messageLabel = new JLabel("", JLabel.CENTER);
385 * Creates a new GPreferences object.
387 public GPreferences()
392 } catch (Exception ex)
394 ex.printStackTrace();
399 * Construct the panel and its tabbed sub-panels.
403 private void jbInit() throws Exception
405 // final JTabbedPane tabbedPane = new JTabbedPane();
406 this.setLayout(new BorderLayout());
408 // message label at top
409 this.add(messageLabel, BorderLayout.NORTH);
411 JPanel okCancelPanel = initOkCancelPanel();
412 this.add(tabbedPane, BorderLayout.CENTER);
413 this.add(okCancelPanel, BorderLayout.SOUTH);
415 tabbedPane.add(initVisualTab(),
416 MessageManager.getString("label.visual"));
418 tabbedPane.add(initColoursTab(),
419 MessageManager.getString("label.colours"));
421 tabbedPane.add(initOverviewTab(),
422 MessageManager.getString("label.overview"));
424 tabbedPane.add(initStructureTab(),
425 MessageManager.getString("label.structure"));
427 tabbedPane.add(initConnectionsTab(),
428 MessageManager.getString("label.connections"));
430 if (!Platform.isJS())
432 tabbedPane.add(initBackupsTab(),
433 MessageManager.getString("label.backups"));
436 tabbedPane.add(initLinksTab(),
437 MessageManager.getString("label.urllinks"));
439 tabbedPane.add(initOutputTab(),
440 MessageManager.getString("label.output"));
442 tabbedPane.add(initEditingTab(),
443 MessageManager.getString("label.editing"));
446 * See WsPreferences for the real work of configuring this tab.
448 if (!Platform.isJS())
450 wsTab.setLayout(new BorderLayout());
451 tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
455 * Handler to validate a tab before leaving it - currently only for
457 * Adding a clearMessage() so messages are cleared when changing tabs.
459 tabbedPane.addChangeListener(new ChangeListener()
461 private Component lastTab;
464 public void stateChanged(ChangeEvent e)
466 if (lastTab == structureTab
467 && tabbedPane.getSelectedComponent() != structureTab)
469 if (!validateStructure())
471 tabbedPane.setSelectedComponent(structureTab);
475 lastTab = tabbedPane.getSelectedComponent();
483 public void setMessage(String message)
487 messageLabel.setText(message);
488 messageLabel.setFont(LABEL_FONT_BOLD);
489 messageLabel.setForeground(Color.RED.darker());
490 messageLabel.revalidate();
491 messageLabel.repaint();
493 // note message not cleared if message is null. call clearMessage()
499 public void clearMessage()
501 // only repaint if message exists
502 if (messageLabel.getText() != null
503 && messageLabel.getText().length() > 0)
505 messageLabel.setText("");
506 messageLabel.revalidate();
507 messageLabel.repaint();
513 public final static int CONNECTIONS_TAB = 5;
515 public void selectTab(int selectTab)
517 // select a given tab - currently only for Connections
520 case CONNECTIONS_TAB:
521 tabbedPane.setSelectedComponent(connectTab);
528 * Initialises the Editing tabbed panel.
532 private JPanel initEditingTab()
534 JPanel editingTab = new JPanel();
535 editingTab.setLayout(null);
536 autoCalculateConsCheck.setFont(LABEL_FONT);
537 autoCalculateConsCheck.setText(
538 MessageManager.getString("label.autocalculate_consensus"));
539 autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
540 padGaps.setFont(LABEL_FONT);
542 MessageManager.getString("label.pad_gaps_when_editing"));
543 padGaps.setBounds(new Rectangle(22, 94, 168, 23));
544 sortByTree.setFont(LABEL_FONT);
546 .setText(MessageManager.getString("label.sort_with_new_tree"));
547 sortByTree.setToolTipText(MessageManager.getString(
548 "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
549 sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
550 editingTab.add(autoCalculateConsCheck);
551 editingTab.add(padGaps);
552 editingTab.add(sortByTree);
557 * Initialises the Output tab
561 private JPanel initOutputTab()
563 JPanel outputTab = new JPanel();
564 outputTab.setLayout(null);
566 JLabel epsLabel = new JLabel(
567 MessageManager.formatMessage("label.rendering_style", "EPS"));
568 epsLabel.setFont(LABEL_FONT);
569 epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
570 epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
571 epsRendering.setFont(LABEL_FONT);
572 epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
573 JLabel htmlLabel = new JLabel(
574 MessageManager.formatMessage("label.rendering_style", "HTML"));
575 htmlLabel.setFont(LABEL_FONT);
576 htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
577 htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
578 htmlRendering.setFont(LABEL_FONT);
579 htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
580 JLabel svgLabel = new JLabel(
581 MessageManager.formatMessage("label.rendering_style", "SVG"));
582 svgLabel.setFont(LABEL_FONT);
583 svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
584 svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
585 svgRendering.setFont(LABEL_FONT);
586 svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
588 JLabel jLabel1 = new JLabel();
589 jLabel1.setFont(LABEL_FONT);
590 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
591 jLabel1.setText(MessageManager.getString("label.append_start_end"));
592 jLabel1.setFont(LABEL_FONT);
594 fastajv.setFont(LABEL_FONT);
595 fastajv.setHorizontalAlignment(SwingConstants.LEFT);
596 clustaljv.setText(MessageManager.getString("label.clustal") + " ");
597 blcjv.setText(MessageManager.getString("label.blc") + " ");
598 fastajv.setText(MessageManager.getString("label.fasta") + " ");
599 msfjv.setText(MessageManager.getString("label.msf") + " ");
600 pfamjv.setText(MessageManager.getString("label.pfam") + " ");
601 pileupjv.setText(MessageManager.getString("label.pileup") + " ");
602 msfjv.setFont(LABEL_FONT);
603 msfjv.setHorizontalAlignment(SwingConstants.LEFT);
604 pirjv.setText(MessageManager.getString("label.pir") + " ");
605 JPanel jPanel11 = new JPanel();
606 jPanel11.setFont(LABEL_FONT);
607 TitledBorder titledBorder2 = new TitledBorder(
608 MessageManager.getString("label.file_output"));
609 jPanel11.setBorder(titledBorder2);
610 jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
611 GridLayout gridLayout3 = new GridLayout();
612 jPanel11.setLayout(gridLayout3);
613 gridLayout3.setRows(8);
614 blcjv.setFont(LABEL_FONT);
615 blcjv.setHorizontalAlignment(SwingConstants.LEFT);
616 clustaljv.setFont(LABEL_FONT);
617 clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
618 pfamjv.setFont(LABEL_FONT);
619 pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
620 pileupjv.setFont(LABEL_FONT);
621 pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
622 pirjv.setFont(LABEL_FONT);
623 pirjv.setHorizontalAlignment(SwingConstants.LEFT);
624 autoIdWidth.setFont(LABEL_FONT);
626 MessageManager.getString("label.automatically_set_id_width"));
627 autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
628 .getString("label.adjusts_width_generated_eps_png")));
629 autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
630 autoIdWidth.addActionListener(new ActionListener()
634 public void actionPerformed(ActionEvent e)
636 autoIdWidth_actionPerformed();
639 userIdWidthlabel.setFont(LABEL_FONT);
640 userIdWidthlabel.setText(
641 MessageManager.getString("label.figure_id_column_width"));
642 userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
643 .getString("label.manually_specify_width_left_column")));
644 userIdWidthlabel.setToolTipText(
645 JvSwingUtils.wrapTooltip(true, MessageManager.getString(
646 "label.manually_specify_width_left_column")));
647 userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
648 userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
649 userIdWidth.setText("");
650 userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
651 userIdWidth.addActionListener(new ActionListener()
655 public void actionPerformed(ActionEvent e)
657 userIdWidth_actionPerformed();
660 modellerOutput.setFont(LABEL_FONT);
662 .setText(MessageManager.getString("label.use_modeller_output"));
663 modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
664 embbedBioJSON.setFont(LABEL_FONT);
665 embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
666 embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
668 jPanel11.add(jLabel1);
670 jPanel11.add(clustaljv);
671 jPanel11.add(fastajv);
673 jPanel11.add(pfamjv);
674 jPanel11.add(pileupjv);
676 outputTab.add(autoIdWidth);
677 outputTab.add(userIdWidth);
678 outputTab.add(userIdWidthlabel);
679 outputTab.add(modellerOutput);
680 if (!Platform.isJS())
683 * JalviewJS doesn't support Lineart option or SVG output
685 outputTab.add(embbedBioJSON);
686 outputTab.add(epsLabel);
687 outputTab.add(epsRendering);
688 outputTab.add(htmlLabel);
689 outputTab.add(htmlRendering);
690 outputTab.add(svgLabel);
691 outputTab.add(svgRendering);
693 outputTab.add(jPanel11);
698 * Initialises the Connections tabbed panel.
702 private JPanel initConnectionsTab()
704 connectTab = new JPanel();
705 connectTab.setLayout(new GridBagLayout());
707 // Label for browser text box
708 JLabel browserLabel = new JLabel();
709 browserLabel.setFont(LABEL_FONT);
710 browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
711 browserLabel.setText(
712 MessageManager.getString("label.default_browser_unix"));
713 defaultBrowser.setFont(LABEL_FONT);
714 defaultBrowser.setText("");
715 final String tooltip = JvSwingUtils.wrapTooltip(true,
716 MessageManager.getString("label.double_click_to_browse"));
717 defaultBrowser.setToolTipText(tooltip);
718 defaultBrowser.addMouseListener(new MouseAdapter()
721 public void mouseClicked(MouseEvent e)
723 if (e.getClickCount() > 1)
725 defaultBrowser_mouseClicked(e);
730 JPanel proxyPanel = initConnTabProxyPanel();
731 initConnTabCheckboxes();
733 // Add default Browser text box
734 connectTab.add(browserLabel,
735 new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
736 GridBagConstraints.WEST, GridBagConstraints.NONE,
737 new Insets(10, 0, 5, 5), 5, 1));
738 defaultBrowser.setFont(LABEL_FONT);
739 defaultBrowser.setText("");
741 connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
742 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
743 new Insets(10, 0, 5, 10), 30, 1));
745 // Add proxy server panel
746 connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
747 GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
748 new Insets(10, 0, 5, 12), 4, 10));
750 // Add usage stats, version check and questionnaire checkboxes
751 connectTab.add(usagestats,
752 new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
753 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
754 new Insets(0, 2, 5, 5), 70, 1));
755 connectTab.add(questionnaire,
756 new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
757 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
758 new Insets(0, 2, 5, 10), 70, 1));
759 connectTab.add(versioncheck,
760 new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
761 GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
762 new Insets(0, 2, 5, 5), 70, 1));
764 versioncheck.setVisible(false);
766 // Add padding so the panel doesn't look ridiculous
767 JPanel spacePanel = new JPanel();
768 connectTab.add(spacePanel,
769 new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
770 GridBagConstraints.WEST, GridBagConstraints.BOTH,
771 new Insets(0, 0, 0, 5), 70, 1));
777 * Initialises the Links tabbed panel.
781 private JPanel initLinksTab()
783 JPanel linkTab = new JPanel();
784 linkTab.setLayout(new GridBagLayout());
786 // Set up table for Url links
787 linkUrlTable.getTableHeader().setReorderingAllowed(false);
788 linkUrlTable.setFillsViewportHeight(true);
789 linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
790 linkUrlTable.setAutoCreateRowSorter(true);
791 linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
793 // adjust row height so radio buttons actually fit
794 // don't do this in the renderer, it causes the awt thread to activate
796 JRadioButton temp = new JRadioButton();
797 linkUrlTable.setRowHeight(temp.getMinimumSize().height);
799 // Table in scrollpane so that the table is given a scrollbar
800 JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
801 linkScrollPane.setBorder(null);
803 // Panel for links functionality
804 JPanel linkPanel = new JPanel(new GridBagLayout());
805 linkPanel.setBorder(new TitledBorder(
806 MessageManager.getString("label.url_linkfrom_sequence_id")));
808 // Put the Url links panel together
810 // Buttons go at top right, resizing only resizes the blank space vertically
811 JPanel buttonPanel = initLinkTabUrlButtons();
812 GridBagConstraints linkConstraints1 = new GridBagConstraints();
813 linkConstraints1.insets = new Insets(0, 0, 5, 0);
814 linkConstraints1.gridx = 0;
815 linkConstraints1.gridy = 0;
816 linkConstraints1.weightx = 1.0;
817 linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
818 linkTab.add(buttonPanel, linkConstraints1);
820 // Links table goes at top left, resizing resizes the table
821 GridBagConstraints linkConstraints2 = new GridBagConstraints();
822 linkConstraints2.insets = new Insets(0, 0, 5, 5);
823 linkConstraints2.gridx = 0;
824 linkConstraints2.gridy = 1;
825 linkConstraints2.weightx = 1.0;
826 linkConstraints2.weighty = 1.0;
827 linkConstraints2.fill = GridBagConstraints.BOTH;
828 linkTab.add(linkScrollPane, linkConstraints2);
830 // Filter box and buttons goes at bottom left, resizing resizes the text box
831 JPanel filterPanel = initLinkTabFilterPanel();
832 GridBagConstraints linkConstraints3 = new GridBagConstraints();
833 linkConstraints3.insets = new Insets(0, 0, 0, 5);
834 linkConstraints3.gridx = 0;
835 linkConstraints3.gridy = 2;
836 linkConstraints3.weightx = 1.0;
837 linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
838 linkTab.add(filterPanel, linkConstraints3);
843 private JPanel initLinkTabFilterPanel()
845 // Filter textbox and reset button
846 JLabel filterLabel = new JLabel(
847 MessageManager.getString("label.filter"));
848 filterLabel.setFont(LABEL_FONT);
849 filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
850 filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
852 filterTB.setFont(LABEL_FONT);
853 filterTB.setText("");
855 doReset.setText(MessageManager.getString("action.showall"));
856 userOnly.setText(MessageManager.getString("action.customfilter"));
858 // Panel for filter functionality
859 JPanel filterPanel = new JPanel(new GridBagLayout());
860 filterPanel.setBorder(new TitledBorder("Filter"));
861 GridBagConstraints gbc = new GridBagConstraints();
864 gbc.fill = GridBagConstraints.NONE;
865 gbc.anchor = GridBagConstraints.WEST;
867 filterPanel.add(filterLabel, gbc);
869 GridBagConstraints gbc1 = new GridBagConstraints();
872 gbc1.fill = GridBagConstraints.HORIZONTAL;
873 gbc1.anchor = GridBagConstraints.WEST;
875 filterPanel.add(filterTB, gbc1);
877 GridBagConstraints gbc2 = new GridBagConstraints();
879 gbc2.fill = GridBagConstraints.NONE;
880 gbc2.anchor = GridBagConstraints.WEST;
881 filterPanel.add(doReset, gbc2);
883 GridBagConstraints gbc3 = new GridBagConstraints();
885 gbc3.fill = GridBagConstraints.NONE;
886 gbc3.anchor = GridBagConstraints.WEST;
887 filterPanel.add(userOnly, gbc3);
892 private JPanel initLinkTabUrlButtons()
894 // Buttons for new / edit / delete Url links
895 JButton newLink = new JButton();
896 newLink.setText(MessageManager.getString("action.new"));
898 editLink.setText(MessageManager.getString("action.edit"));
900 deleteLink.setText(MessageManager.getString("action.delete"));
902 // no current selection, so initially disable delete/edit buttons
903 editLink.setEnabled(false);
904 deleteLink.setEnabled(false);
906 newLink.addActionListener(new java.awt.event.ActionListener()
909 public void actionPerformed(ActionEvent e)
911 newLink_actionPerformed(e);
915 editLink.setText(MessageManager.getString("action.edit"));
916 editLink.addActionListener(new java.awt.event.ActionListener()
919 public void actionPerformed(ActionEvent e)
921 editLink_actionPerformed(e);
925 deleteLink.setText(MessageManager.getString("action.delete"));
926 deleteLink.addActionListener(new java.awt.event.ActionListener()
929 public void actionPerformed(ActionEvent e)
931 deleteLink_actionPerformed(e);
935 JPanel buttonPanel = new JPanel(new GridBagLayout());
936 buttonPanel.setBorder(new TitledBorder("Edit links"));
937 GridBagConstraints gbc = new GridBagConstraints();
940 gbc.fill = GridBagConstraints.NONE;
941 buttonPanel.add(newLink, gbc);
943 GridBagConstraints gbc1 = new GridBagConstraints();
946 gbc1.fill = GridBagConstraints.NONE;
947 buttonPanel.add(editLink, gbc1);
949 GridBagConstraints gbc2 = new GridBagConstraints();
952 gbc2.fill = GridBagConstraints.NONE;
953 buttonPanel.add(deleteLink, gbc2);
955 GridBagConstraints gbc3 = new GridBagConstraints();
958 gbc3.fill = GridBagConstraints.HORIZONTAL;
960 JPanel spacePanel = new JPanel();
961 spacePanel.setBorder(null);
962 buttonPanel.add(spacePanel, gbc3);
968 * Initialises the proxy server panel in the Connections tab
970 * @return the proxy server panel
972 private JPanel initConnTabProxyPanel()
974 // Label for server text box
975 serverLabel.setText(MessageManager.getString("label.host") + ": ");
976 serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
977 serverLabel.setFont(LABEL_FONT);
978 serverLabel2.setText(MessageManager.getString("label.host") + ": ");
979 serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
980 serverLabel2.setFont(LABEL_FONT);
982 // Proxy server and port text boxes
983 proxyServerHttpTB.setFont(LABEL_FONT);
984 proxyServerHttpTB.setColumns(40);
985 proxyPortHttpTB.setFont(LABEL_FONT);
986 proxyPortHttpTB.setColumns(4);
987 proxyServerHttpsTB.setFont(LABEL_FONT);
988 proxyServerHttpsTB.setColumns(40);
989 proxyPortHttpsTB.setFont(LABEL_FONT);
990 proxyPortHttpsTB.setColumns(4);
991 proxyAuthUsernameTB.setFont(LABEL_FONT);
992 proxyAuthUsernameTB.setColumns(30);
994 // check for any change to enable applyProxyButton
995 DocumentListener d = new DocumentListener()
998 public void changedUpdate(DocumentEvent e)
1000 applyProxyButtonEnabled(true);
1004 public void insertUpdate(DocumentEvent e)
1006 applyProxyButtonEnabled(true);
1010 public void removeUpdate(DocumentEvent e)
1012 applyProxyButtonEnabled(true);
1015 proxyServerHttpTB.getDocument().addDocumentListener(d);
1016 proxyPortHttpTB.getDocument().addDocumentListener(d);
1017 proxyServerHttpsTB.getDocument().addDocumentListener(d);
1018 proxyPortHttpsTB.getDocument().addDocumentListener(d);
1019 proxyAuthUsernameTB.getDocument().addDocumentListener(d);
1020 proxyAuthPasswordPB.setFont(LABEL_FONT);
1021 proxyAuthPasswordPB.setColumns(30);
1022 proxyAuthPasswordPB.getDocument()
1023 .addDocumentListener(new DocumentListener()
1026 public void changedUpdate(DocumentEvent e)
1028 proxyAuthPasswordCheckHighlight(true);
1029 applyProxyButtonEnabled(true);
1033 public void insertUpdate(DocumentEvent e)
1035 proxyAuthPasswordCheckHighlight(true);
1036 applyProxyButtonEnabled(true);
1040 public void removeUpdate(DocumentEvent e)
1042 proxyAuthPasswordCheckHighlight(true);
1043 applyProxyButtonEnabled(true);
1048 // Label for Port text box
1049 portLabel.setFont(LABEL_FONT);
1050 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1051 portLabel.setText(MessageManager.getString("label.port") + ": ");
1052 portLabel2.setFont(LABEL_FONT);
1053 portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
1054 portLabel2.setText(MessageManager.getString("label.port") + ": ");
1056 httpLabel.setText("HTTP");
1057 httpLabel.setFont(LABEL_FONT_BOLD);
1058 httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
1059 httpsLabel.setText("HTTPS");
1060 httpsLabel.setFont(LABEL_FONT_BOLD);
1061 httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
1063 proxyAuthUsernameLabel
1064 .setText(MessageManager.getString("label.username") + ": ");
1065 proxyAuthUsernameLabel.setFont(LABEL_FONT);
1066 proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1067 proxyAuthPasswordLabel
1068 .setText(MessageManager.getString("label.password") + ": ");
1069 proxyAuthPasswordLabel.setFont(LABEL_FONT);
1070 proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1071 passwordNotStoredLabel.setText(
1072 "(" + MessageManager.getString("label.not_stored") + ")");
1073 passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
1074 passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
1076 // Proxy type radio buttons
1077 noProxy.setFont(LABEL_FONT);
1078 noProxy.setHorizontalAlignment(SwingConstants.LEFT);
1079 noProxy.setText(MessageManager.getString("label.no_proxy"));
1080 systemProxy.setFont(LABEL_FONT);
1081 systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
1082 systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
1083 displayUserHostPort(Cache.startupProxyProperties[4],
1084 Cache.startupProxyProperties[0],
1085 Cache.startupProxyProperties[1]),
1086 displayUserHostPort(Cache.startupProxyProperties[6],
1087 Cache.startupProxyProperties[2],
1088 Cache.startupProxyProperties[3])));
1089 customProxy.setFont(LABEL_FONT);
1090 customProxy.setHorizontalAlignment(SwingConstants.LEFT);
1091 customProxy.setText(
1092 MessageManager.getString("label.use_proxy_server") + ":");
1093 ActionListener al = new ActionListener()
1096 public void actionPerformed(ActionEvent e)
1098 proxyType_actionPerformed();
1101 noProxy.addActionListener(al);
1102 systemProxy.addActionListener(al);
1103 customProxy.addActionListener(al);
1104 proxyType.add(noProxy);
1105 proxyType.add(systemProxy);
1106 proxyType.add(customProxy);
1108 proxyAuth.setFont(LABEL_FONT);
1109 proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
1110 proxyAuth.setText(MessageManager.getString("label.auth_required"));
1111 proxyAuth.addActionListener(new ActionListener()
1114 public void actionPerformed(ActionEvent e)
1116 proxyAuth_actionPerformed();
1120 setCustomProxyEnabled();
1122 // Make proxy server panel
1123 JPanel proxyPanel = new JPanel();
1124 TitledBorder titledBorder1 = new TitledBorder(
1125 MessageManager.getString("label.proxy_servers"));
1126 proxyPanel.setBorder(titledBorder1);
1127 proxyPanel.setLayout(new GridBagLayout());
1128 GridBagConstraints gbc = new GridBagConstraints();
1129 gbc.fill = GridBagConstraints.HORIZONTAL;
1132 GridBagConstraints c = new GridBagConstraints();
1133 // Proxy type radio buttons (3)
1134 JPanel ptPanel = new JPanel();
1135 ptPanel.setLayout(new GridBagLayout());
1140 c.fill = GridBagConstraints.HORIZONTAL;
1141 ptPanel.add(noProxy, c);
1143 ptPanel.add(systemProxy, c);
1145 ptPanel.add(customProxy, c);
1148 proxyPanel.add(ptPanel, gbc);
1150 // host and port text boxes
1151 JPanel hpPanel = new JPanel();
1152 hpPanel.setLayout(new GridBagLayout());
1153 // HTTP host port row
1158 c.anchor = GridBagConstraints.LINE_START;
1159 hpPanel.add(httpLabel, c);
1163 c.anchor = GridBagConstraints.LINE_END;
1164 hpPanel.add(serverLabel, c);
1168 c.anchor = GridBagConstraints.LINE_START;
1169 hpPanel.add(proxyServerHttpTB, c);
1173 c.anchor = GridBagConstraints.LINE_END;
1174 hpPanel.add(portLabel, c);
1178 c.anchor = GridBagConstraints.LINE_START;
1179 hpPanel.add(proxyPortHttpTB, c);
1181 // HTTPS host port row
1186 c.anchor = GridBagConstraints.LINE_START;
1187 hpPanel.add(httpsLabel, c);
1190 c.anchor = GridBagConstraints.LINE_END;
1191 hpPanel.add(serverLabel2, c);
1194 c.anchor = GridBagConstraints.LINE_START;
1195 hpPanel.add(proxyServerHttpsTB, c);
1198 c.anchor = GridBagConstraints.LINE_END;
1199 hpPanel.add(portLabel2, c);
1202 c.anchor = GridBagConstraints.LINE_START;
1203 hpPanel.add(proxyPortHttpsTB, c);
1206 proxyPanel.add(hpPanel, gbc);
1208 if (!Platform.isJS())
1210 * java.net.Authenticator is not implemented in SwingJS. Not displaying the
1211 * Authentication options in Preferences.
1217 // Require authentication checkbox
1219 proxyPanel.add(proxyAuth, gbc);
1221 // username and password
1222 JPanel upPanel = new JPanel();
1223 upPanel.setLayout(new GridBagLayout());
1229 c.anchor = GridBagConstraints.LINE_END;
1230 upPanel.add(proxyAuthUsernameLabel, c);
1234 c.anchor = GridBagConstraints.LINE_START;
1235 upPanel.add(proxyAuthUsernameTB, c);
1241 c.anchor = GridBagConstraints.LINE_END;
1242 upPanel.add(proxyAuthPasswordLabel, c);
1246 c.anchor = GridBagConstraints.LINE_START;
1247 upPanel.add(proxyAuthPasswordPB, c);
1251 c.anchor = GridBagConstraints.LINE_START;
1252 upPanel.add(passwordNotStoredLabel, c);
1255 proxyPanel.add(upPanel, gbc);
1259 applyProxyButton.setText(MessageManager.getString("action.apply"));
1260 applyProxyButton.addActionListener(new ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 saveProxySettings();
1266 applyProxyButton.setEnabled(false);
1270 gbc.fill = GridBagConstraints.NONE;
1271 gbc.anchor = GridBagConstraints.LINE_END;
1272 proxyPanel.add(applyProxyButton, gbc);
1277 public void proxyAuthPasswordCheckHighlight(boolean enabled)
1279 proxyAuthPasswordCheckHighlight(enabled, false);
1282 public void proxyAuthPasswordCheckHighlight(boolean enabled,
1285 if (enabled && proxyType.isSelected(customProxy.getModel())
1286 && proxyAuth.isSelected()
1287 && !proxyAuthUsernameTB.getText().isEmpty()
1288 && proxyAuthPasswordPB.getDocument().getLength() == 0)
1291 proxyAuthPasswordPB.grabFocus();
1292 proxyAuthPasswordPB.setBackground(Color.PINK);
1296 proxyAuthPasswordPB.setBackground(Color.WHITE);
1300 public void applyProxyButtonEnabled(boolean enabled)
1302 applyProxyButton.setEnabled(enabled);
1305 public void saveProxySettings()
1307 // overridden in Preferences
1310 private String displayUserHostPort(String user, String host, String port)
1312 boolean hostBlank = (host == null || host.isEmpty());
1313 boolean portBlank = (port == null || port.isEmpty());
1314 if (hostBlank && portBlank)
1316 return MessageManager.getString("label.none");
1319 StringBuilder sb = new StringBuilder();
1322 sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
1326 sb.append(hostBlank ? "" : host);
1332 return sb.toString();
1336 * Initialises the checkboxes in the Connections tab
1338 private void initConnTabCheckboxes()
1340 // Usage stats checkbox label
1342 MessageManager.getString("label.send_usage_statistics"));
1343 usagestats.setFont(LABEL_FONT);
1344 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1345 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1347 // Questionnaire checkbox label
1348 questionnaire.setText(
1349 MessageManager.getString("label.check_for_questionnaires"));
1350 questionnaire.setFont(LABEL_FONT);
1351 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1352 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1354 // Check for latest version checkbox label
1355 versioncheck.setText(
1356 MessageManager.getString("label.check_for_latest_version"));
1357 versioncheck.setFont(LABEL_FONT);
1358 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1359 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1363 * Initialises the parent panel which contains the tabbed sections.
1367 private JPanel initOkCancelPanel()
1369 JButton ok = new JButton();
1370 ok.setText(MessageManager.getString("action.ok"));
1371 ok.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 ok_actionPerformed(e);
1379 JButton cancel = new JButton();
1380 cancel.setText(MessageManager.getString("action.cancel"));
1381 cancel.addActionListener(new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 cancel_actionPerformed(e);
1389 JPanel okCancelPanel = new JPanel();
1390 okCancelPanel.add(ok);
1391 okCancelPanel.add(cancel);
1392 return okCancelPanel;
1396 * Initialises the Colours tabbed panel.
1400 private JPanel initColoursTab()
1402 JPanel coloursTab = new JPanel();
1403 coloursTab.setBorder(new TitledBorder(
1404 MessageManager.getString("action.open_new_alignment")));
1405 coloursTab.setLayout(new FlowLayout());
1406 JLabel mincolourLabel = new JLabel();
1407 mincolourLabel.setFont(LABEL_FONT);
1408 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1409 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1410 minColour.setFont(LABEL_FONT);
1411 minColour.setBorder(BorderFactory.createEtchedBorder());
1412 minColour.setPreferredSize(new Dimension(40, 20));
1413 minColour.addMouseListener(new MouseAdapter()
1416 public void mousePressed(MouseEvent e)
1418 minColour_actionPerformed(minColour);
1421 JLabel maxcolourLabel = new JLabel();
1422 maxcolourLabel.setFont(LABEL_FONT);
1423 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1424 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1425 maxColour.setFont(LABEL_FONT);
1426 maxColour.setBorder(BorderFactory.createEtchedBorder());
1427 maxColour.setPreferredSize(new Dimension(40, 20));
1428 maxColour.addMouseListener(new MouseAdapter()
1431 public void mousePressed(MouseEvent e)
1433 maxColour_actionPerformed(maxColour);
1437 protColour.setFont(LABEL_FONT);
1438 protColour.setBounds(new Rectangle(172, 225, 155, 21));
1439 JLabel protColourLabel = new JLabel();
1440 protColourLabel.setFont(LABEL_FONT);
1441 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1442 protColourLabel.setText(
1443 MessageManager.getString("label.prot_alignment_colour") + " ");
1444 JvSwingUtils.addtoLayout(coloursTab,
1446 .getString("label.default_colour_scheme_for_alignment"),
1447 protColourLabel, protColour);
1449 nucColour.setFont(LABEL_FONT);
1450 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1451 JLabel nucColourLabel = new JLabel();
1452 nucColourLabel.setFont(LABEL_FONT);
1453 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1454 nucColourLabel.setText(
1455 MessageManager.getString("label.nuc_alignment_colour") + " ");
1456 JvSwingUtils.addtoLayout(coloursTab,
1458 .getString("label.default_colour_scheme_for_alignment"),
1459 nucColourLabel, nucColour);
1461 JPanel annotationShding = new JPanel();
1462 annotationShding.setBorder(new TitledBorder(
1463 MessageManager.getString("label.annotation_shading_default")));
1464 annotationShding.setLayout(new GridLayout(1, 2));
1465 JvSwingUtils.addtoLayout(annotationShding,
1466 MessageManager.getString(
1467 "label.default_minimum_colour_annotation_shading"),
1468 mincolourLabel, minColour);
1469 JvSwingUtils.addtoLayout(annotationShding,
1470 MessageManager.getString(
1471 "label.default_maximum_colour_annotation_shading"),
1472 maxcolourLabel, maxColour);
1473 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1478 * Initialises the Overview tabbed panel.
1482 private JPanel initOverviewTab()
1484 JPanel overviewPanel = new JPanel();
1485 overviewPanel.setBorder(new TitledBorder(
1486 MessageManager.getString("label.overview_settings")));
1488 gapColour.setFont(LABEL_FONT);
1489 // fixing the border colours stops apparent colour bleed from the panel
1490 gapColour.setBorder(
1491 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1492 gapColour.setPreferredSize(new Dimension(40, 20));
1493 gapColour.addMouseListener(new MouseAdapter()
1496 public void mousePressed(MouseEvent e)
1498 gapColour_actionPerformed(gapColour);
1502 hiddenColour.setFont(LABEL_FONT);
1503 // fixing the border colours stops apparent colour bleed from the panel
1504 hiddenColour.setBorder(
1505 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1506 hiddenColour.setPreferredSize(new Dimension(40, 20));
1507 hiddenColour.addMouseListener(new MouseAdapter()
1510 public void mousePressed(MouseEvent e)
1512 hiddenColour_actionPerformed(hiddenColour);
1516 useLegacyGap = new JCheckBox(
1517 MessageManager.getString("label.ov_legacy_gap"));
1518 useLegacyGap.setFont(LABEL_FONT);
1519 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1520 useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1521 gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1522 gapLabel.setFont(LABEL_FONT);
1523 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1524 gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1525 showHiddenAtStart = new JCheckBox(
1526 MessageManager.getString("label.ov_show_hide_default"));
1527 showHiddenAtStart.setFont(LABEL_FONT);
1528 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1529 showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1530 JLabel hiddenLabel = new JLabel(
1531 MessageManager.getString("label.hidden_colour"));
1532 hiddenLabel.setFont(LABEL_FONT);
1533 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1534 hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1536 useLegacyGap.addActionListener(new ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 useLegacyGaps_actionPerformed(e);
1545 overviewPanel.setLayout(new GridBagLayout());
1546 GridBagConstraints c1 = new GridBagConstraints();
1548 c1.fill = GridBagConstraints.HORIZONTAL;
1553 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1554 overviewPanel.add(useLegacyGap, c1);
1556 GridBagConstraints c2 = new GridBagConstraints();
1557 c2.fill = GridBagConstraints.HORIZONTAL;
1560 c2.insets = new Insets(0, 15, 0, 10);
1561 overviewPanel.add(gapLabel, c2);
1563 GridBagConstraints c3 = new GridBagConstraints();
1564 c3.fill = GridBagConstraints.HORIZONTAL;
1567 c3.insets = new Insets(0, 0, 0, 15);
1568 overviewPanel.add(gapColour, c3);
1570 GridBagConstraints c4 = new GridBagConstraints();
1571 c4.fill = GridBagConstraints.HORIZONTAL;
1575 overviewPanel.add(showHiddenAtStart, c4);
1577 GridBagConstraints c5 = new GridBagConstraints();
1578 c5.fill = GridBagConstraints.HORIZONTAL;
1581 c5.insets = new Insets(0, 15, 0, 10);
1582 overviewPanel.add(hiddenLabel, c5);
1584 GridBagConstraints c6 = new GridBagConstraints();
1585 c6.fill = GridBagConstraints.HORIZONTAL;
1588 c6.insets = new Insets(0, 0, 0, 15);
1589 overviewPanel.add(hiddenColour, c6);
1591 JButton resetButton = new JButton(
1592 MessageManager.getString("label.reset_to_defaults"));
1594 resetButton.addActionListener(new ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 resetOvDefaults_actionPerformed(e);
1603 GridBagConstraints c7 = new GridBagConstraints();
1604 c7.fill = GridBagConstraints.NONE;
1607 c7.insets = new Insets(10, 0, 0, 0);
1608 c7.anchor = GridBagConstraints.WEST;
1609 overviewPanel.add(resetButton, c7);
1611 // Add padding so the panel doesn't look ridiculous
1612 JPanel spacePanel = new JPanel();
1613 overviewPanel.add(spacePanel,
1614 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1615 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1616 new Insets(0, 0, 0, 5), 0, 0));
1618 return overviewPanel;
1622 * Initialises the Structure tabbed panel.
1626 private JPanel initStructureTab()
1628 structureTab = new JPanel();
1630 structureTab.setBorder(new TitledBorder(
1631 MessageManager.getString("label.structure_options")));
1632 structureTab.setLayout(null);
1633 final int width = 420;
1634 final int height = 22;
1635 final int lineSpacing = 25;
1638 structFromPdb.setFont(LABEL_FONT);
1640 .setText(MessageManager.getString("label.struct_from_pdb"));
1641 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1642 structFromPdb.addActionListener(new ActionListener()
1645 public void actionPerformed(ActionEvent e)
1647 boolean selected = structFromPdb.isSelected();
1648 // enable other options only when the first is checked
1649 useRnaView.setEnabled(selected);
1650 addSecondaryStructure.setEnabled(selected);
1651 addTempFactor.setEnabled(selected);
1654 structureTab.add(structFromPdb);
1656 // indent checkboxes that are conditional on the first one
1657 ypos += lineSpacing;
1658 useRnaView.setFont(LABEL_FONT);
1659 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1660 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1661 structureTab.add(useRnaView);
1663 ypos += lineSpacing;
1664 addSecondaryStructure.setFont(LABEL_FONT);
1665 addSecondaryStructure
1666 .setText(MessageManager.getString("label.autoadd_secstr"));
1667 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1668 structureTab.add(addSecondaryStructure);
1670 ypos += lineSpacing;
1671 addTempFactor.setFont(LABEL_FONT);
1672 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1673 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1674 structureTab.add(addTempFactor);
1676 ypos += lineSpacing;
1677 JLabel viewerLabel = new JLabel();
1678 viewerLabel.setFont(LABEL_FONT);
1679 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1680 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1681 viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
1682 structureTab.add(viewerLabel);
1685 * add all external viewers as options here - check
1686 * when selected whether the program is installed
1688 structViewer.setFont(LABEL_FONT);
1689 structViewer.setBounds(new Rectangle(190, ypos, 120, height));
1690 structViewer.addItem(ViewerType.JMOL.name());
1691 structViewer.addItem(ViewerType.CHIMERA.name());
1692 structViewer.addItem(ViewerType.CHIMERAX.name());
1693 structViewer.addItem(ViewerType.PYMOL.name());
1694 structViewer.addActionListener(new ActionListener()
1697 public void actionPerformed(ActionEvent e)
1699 structureViewer_actionPerformed(
1700 (String) structViewer.getSelectedItem());
1703 structureTab.add(structViewer);
1705 ypos += lineSpacing;
1706 structureViewerPathLabel = new JLabel();
1707 structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0,
1709 structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1710 structureViewerPathLabel.setText(MessageManager
1711 .formatMessage("label.viewer_path", "Chimera(X)"));
1712 structureViewerPathLabel
1713 .setBounds(new Rectangle(10, ypos, 170, height));
1714 structureViewerPathLabel.setEnabled(false);
1715 structureTab.add(structureViewerPathLabel);
1717 structureViewerPath.setFont(LABEL_FONT);
1718 structureViewerPath.setText("");
1719 structureViewerPath.setEnabled(false);
1720 final String tooltip = JvSwingUtils.wrapTooltip(true,
1721 MessageManager.getString("label.viewer_path_tip"));
1722 structureViewerPath.setToolTipText(tooltip);
1723 structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
1724 structureViewerPath.addMouseListener(new MouseAdapter()
1727 public void mouseClicked(MouseEvent e)
1729 if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
1731 String chosen = openFileChooser();
1734 structureViewerPath.setText(chosen);
1739 structureTab.add(structureViewerPath);
1741 ypos += lineSpacing;
1742 nwMapping.setFont(LABEL_FONT);
1743 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1744 siftsMapping.setFont(LABEL_FONT);
1745 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1746 mappingMethod.add(nwMapping);
1747 mappingMethod.add(siftsMapping);
1748 JPanel mappingPanel = new JPanel();
1749 mappingPanel.setFont(LABEL_FONT);
1750 TitledBorder mmTitledBorder = new TitledBorder(
1751 MessageManager.getString("label.mapping_method"));
1752 mmTitledBorder.setTitleFont(LABEL_FONT);
1753 mappingPanel.setBorder(mmTitledBorder);
1754 mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
1755 // GridLayout mappingLayout = new GridLayout();
1756 mappingPanel.setLayout(new GridLayout());
1757 mappingPanel.add(nwMapping);
1758 mappingPanel.add(siftsMapping);
1759 structureTab.add(mappingPanel);
1761 ypos += lineSpacing;
1762 ypos += lineSpacing;
1763 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1764 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1765 docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
1766 structureTab.add(docFieldPref);
1769 * hide Chimera options in JalviewJS
1771 if (Platform.isJS())
1773 structureViewerPathLabel.setVisible(false);
1774 structureViewerPath.setVisible(false);
1775 viewerLabel.setVisible(false);
1776 structViewer.setVisible(false);
1779 return structureTab;
1783 * Action on choosing a structure viewer from combobox options.
1785 * @param selectedItem
1787 protected void structureViewer_actionPerformed(String selectedItem)
1792 * Show a dialog for the user to choose a file. Returns the chosen path, or
1797 protected String openFileChooser()
1799 String choice = null;
1800 JFileChooser chooser = new JFileChooser();
1802 // chooser.setFileView(new JalviewFileView());
1803 chooser.setDialogTitle(
1804 MessageManager.getString("label.open_local_file"));
1805 chooser.setToolTipText(MessageManager.getString("action.open"));
1807 int value = chooser.showOpenDialog(this);
1809 if (value == JFileChooser.APPROVE_OPTION)
1811 choice = chooser.getSelectedFile().getPath();
1817 * Validate the structure tab preferences; if invalid, set focus on this tab.
1821 protected boolean validateStructure(FocusEvent e)
1823 if (!validateStructure())
1825 e.getComponent().requestFocusInWindow();
1831 protected boolean validateStructure()
1837 * Initialises the Visual tabbed panel.
1841 private JPanel initVisualTab()
1843 JPanel visualTab = new JPanel();
1844 visualTab.setBorder(new TitledBorder(
1845 MessageManager.getString("action.open_new_alignment")));
1846 visualTab.setLayout(null);
1847 fullScreen.setFont(LABEL_FONT);
1848 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1849 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1850 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1851 quality.setEnabled(false);
1852 quality.setFont(LABEL_FONT);
1853 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1854 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1855 quality.setSelected(true);
1856 quality.setText(MessageManager.getString("label.quality"));
1857 conservation.setEnabled(false);
1858 conservation.setFont(LABEL_FONT);
1859 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1860 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1861 conservation.setSelected(true);
1862 conservation.setText(MessageManager.getString("label.conservation"));
1863 identity.setEnabled(false);
1864 identity.setFont(LABEL_FONT);
1865 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1866 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1867 identity.setSelected(true);
1868 identity.setText(MessageManager.getString("label.consensus"));
1869 showOccupancy.setFont(LABEL_FONT);
1870 showOccupancy.setEnabled(false);
1871 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1872 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1873 showOccupancy.setSelected(true);
1874 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1876 JLabel showGroupbits = new JLabel();
1877 showGroupbits.setFont(LABEL_FONT);
1878 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1879 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1881 .setText(MessageManager.getString("action.show_group") + ":");
1882 JLabel showConsensbits = new JLabel();
1883 showConsensbits.setFont(LABEL_FONT);
1884 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1885 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1887 .setText(MessageManager.getString("label.consensus") + ":");
1888 showConsensHistogram.setEnabled(false);
1889 showConsensHistogram.setFont(LABEL_FONT);
1890 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1891 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1892 showConsensHistogram.setSelected(true);
1893 showConsensHistogram
1894 .setText(MessageManager.getString("label.histogram"));
1895 showConsensLogo.setEnabled(false);
1896 showConsensLogo.setFont(LABEL_FONT);
1897 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1898 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1899 showConsensLogo.setSelected(true);
1900 showConsensLogo.setText(MessageManager.getString("label.logo"));
1901 showGroupConsensus.setEnabled(false);
1902 showGroupConsensus.setFont(LABEL_FONT);
1903 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1904 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1905 showGroupConsensus.setSelected(true);
1906 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1907 showGroupConservation.setEnabled(false);
1908 showGroupConservation.setFont(LABEL_FONT);
1909 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1910 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1911 showGroupConservation.setSelected(true);
1912 showGroupConservation
1913 .setText(MessageManager.getString("label.conservation"));
1914 showNpTooltip.setEnabled(true);
1915 showNpTooltip.setFont(LABEL_FONT);
1916 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1917 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1918 showNpTooltip.setSelected(true);
1919 showNpTooltip.setText(
1920 MessageManager.getString("label.non_positional_features"));
1921 showDbRefTooltip.setEnabled(true);
1922 showDbRefTooltip.setFont(LABEL_FONT);
1923 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1924 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1925 showDbRefTooltip.setSelected(true);
1927 .setText(MessageManager.getString("label.database_references"));
1928 annotations.setFont(LABEL_FONT);
1929 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1930 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1931 annotations.setSelected(true);
1932 annotations.setText(MessageManager.getString("label.show_annotations"));
1933 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1934 annotations.addActionListener(new ActionListener()
1937 public void actionPerformed(ActionEvent e)
1939 annotations_actionPerformed(e);
1942 identity.addActionListener(new ActionListener()
1945 public void actionPerformed(ActionEvent e)
1947 annotations_actionPerformed(e);
1950 showGroupConsensus.addActionListener(new ActionListener()
1953 public void actionPerformed(ActionEvent e)
1955 annotations_actionPerformed(e);
1958 showUnconserved.setFont(LABEL_FONT);
1959 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1960 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1961 showUnconserved.setSelected(true);
1963 .setText(MessageManager.getString("action.show_unconserved"));
1964 showUnconserved.addActionListener(new ActionListener()
1967 public void actionPerformed(ActionEvent e)
1969 showunconserved_actionPerformed(e);
1973 // TODO these are not yet added to / action from Preferences
1974 // JCheckBox shareSelections = new JCheckBox();
1975 // shareSelections.setFont(verdana11);
1976 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1977 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1978 // shareSelections.setSelected(true);
1979 // shareSelections.setText(MessageManager
1980 // .getString("label.share_selection_across_views"));
1981 // JCheckBox followHighlight = new JCheckBox();
1982 // followHighlight.setFont(verdana11);
1983 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1984 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1985 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1986 // followHighlight.setSelected(true);
1987 // followHighlight.setText(MessageManager
1988 // .getString("label.scroll_highlighted_regions"));
1990 seqLimit.setFont(LABEL_FONT);
1991 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1992 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1993 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1994 smoothFont.setFont(LABEL_FONT);
1995 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1996 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1997 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1998 scaleProteinToCdna.setFont(LABEL_FONT);
1999 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
2000 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
2001 scaleProteinToCdna.setText(
2002 MessageManager.getString("label.scale_protein_to_cdna"));
2003 scaleProteinToCdna.setToolTipText(
2004 MessageManager.getString("label.scale_protein_to_cdna_tip"));
2005 JLabel gapLabel = new JLabel();
2006 gapLabel.setFont(LABEL_FONT);
2007 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2008 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
2009 JLabel fontLabel = new JLabel();
2010 fontLabel.setFont(LABEL_FONT);
2011 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2012 fontLabel.setText(MessageManager.getString("label.font"));
2013 fontSizeCB.setFont(LABEL_FONT);
2014 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
2015 fontStyleCB.setFont(LABEL_FONT);
2016 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
2017 fontNameCB.setFont(LABEL_FONT);
2018 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
2019 gapSymbolCB.setFont(LABEL_FONT);
2020 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
2021 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
2022 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
2023 gapSymbolCB.setRenderer(dlcr);
2025 startupCheckbox.setText(MessageManager.getString("action.open_file"));
2026 startupCheckbox.setFont(LABEL_FONT);
2027 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
2028 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
2029 startupCheckbox.setSelected(true);
2030 startupFileTextfield.setFont(LABEL_FONT);
2031 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
2032 final String tooltip = JvSwingUtils.wrapTooltip(true,
2033 MessageManager.getString("label.double_click_to_browse"));
2034 startupFileTextfield.setToolTipText(tooltip);
2035 startupFileTextfield.addMouseListener(new MouseAdapter()
2038 public void mouseClicked(MouseEvent e)
2040 if (e.getClickCount() > 1)
2042 startupFileTextfield_mouseClicked();
2047 sortby.setFont(LABEL_FONT);
2048 sortby.setBounds(new Rectangle(172, 260, 155, 21));
2049 JLabel sortLabel = new JLabel();
2050 sortLabel.setFont(LABEL_FONT);
2051 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2052 sortLabel.setText(MessageManager.getString("label.sort_by"));
2053 sortAnnBy.setFont(LABEL_FONT);
2054 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
2055 JLabel sortAnnLabel = new JLabel();
2056 sortAnnLabel.setFont(LABEL_FONT);
2057 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2058 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
2059 sortAutocalc.setFont(LABEL_FONT);
2060 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
2062 JPanel annsettingsPanel = new JPanel();
2063 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
2064 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
2065 annsettingsPanel.setBorder(new EtchedBorder());
2066 visualTab.add(annsettingsPanel);
2067 Border jb = new EmptyBorder(1, 1, 4, 5);
2068 annotations.setBorder(jb);
2069 showOccupancy.setBorder(jb);
2070 quality.setBorder(jb);
2071 conservation.setBorder(jb);
2072 identity.setBorder(jb);
2073 showConsensbits.setBorder(jb);
2074 showGroupbits.setBorder(jb);
2075 showGroupConsensus.setBorder(jb);
2076 showGroupConservation.setBorder(jb);
2077 showConsensHistogram.setBorder(jb);
2078 showConsensLogo.setBorder(jb);
2080 JPanel autoAnnotSettings = new JPanel();
2081 annsettingsPanel.add(autoAnnotSettings);
2082 autoAnnotSettings.setLayout(new GridLayout(0, 2));
2083 autoAnnotSettings.add(annotations);
2084 autoAnnotSettings.add(quality);
2085 // second row of autoannotation box
2086 autoAnnotSettings = new JPanel();
2087 annsettingsPanel.add(autoAnnotSettings);
2089 autoAnnotSettings.setLayout(new GridLayout(0, 3));
2090 autoAnnotSettings.add(conservation);
2091 autoAnnotSettings.add(identity);
2092 autoAnnotSettings.add(showOccupancy);
2093 autoAnnotSettings.add(showGroupbits);
2094 autoAnnotSettings.add(showGroupConservation);
2095 autoAnnotSettings.add(showGroupConsensus);
2096 autoAnnotSettings.add(showConsensbits);
2097 autoAnnotSettings.add(showConsensHistogram);
2098 autoAnnotSettings.add(showConsensLogo);
2100 JPanel tooltipSettings = new JPanel();
2101 tooltipSettings.setBorder(new TitledBorder(
2102 MessageManager.getString("label.sequence_id_tooltip")));
2103 tooltipSettings.setBounds(173, 140, 220, 62);
2104 tooltipSettings.setLayout(new GridLayout(2, 1));
2105 tooltipSettings.add(showDbRefTooltip);
2106 tooltipSettings.add(showNpTooltip);
2107 visualTab.add(tooltipSettings);
2109 wrap.setFont(LABEL_FONT);
2110 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
2111 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
2112 wrap.setText(MessageManager.getString("label.wrap_alignment"));
2113 rightAlign.setFont(LABEL_FONT);
2114 rightAlign.setForeground(Color.black);
2115 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
2116 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
2117 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
2118 idItalics.setFont(LABEL_FONT_ITALIC);
2119 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
2120 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
2122 MessageManager.getString("label.sequence_name_italics"));
2123 openoverv.setFont(LABEL_FONT);
2124 openoverv.setActionCommand(
2125 MessageManager.getString("label.open_overview"));
2126 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
2127 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
2128 openoverv.setText(MessageManager.getString("label.open_overview"));
2129 JPanel jPanel2 = new JPanel();
2130 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
2131 jPanel2.setLayout(new GridLayout(14, 1));
2132 jPanel2.add(fullScreen);
2133 jPanel2.add(openoverv);
2134 jPanel2.add(seqLimit);
2135 jPanel2.add(rightAlign);
2136 jPanel2.add(fontLabel);
2137 jPanel2.add(showUnconserved);
2138 jPanel2.add(idItalics);
2139 jPanel2.add(smoothFont);
2140 jPanel2.add(scaleProteinToCdna);
2141 jPanel2.add(gapLabel);
2143 jPanel2.add(sortLabel);
2144 jPanel2.add(sortAnnLabel);
2145 jPanel2.add(startupCheckbox);
2146 visualTab.add(jPanel2);
2147 visualTab.add(startupFileTextfield);
2148 visualTab.add(sortby);
2149 visualTab.add(sortAnnBy);
2150 visualTab.add(sortAutocalc);
2151 visualTab.add(gapSymbolCB);
2152 visualTab.add(fontNameCB);
2153 visualTab.add(fontSizeCB);
2154 visualTab.add(fontStyleCB);
2156 if (Platform.isJS())
2158 startupCheckbox.setVisible(false);
2159 startupFileTextfield.setVisible(false);
2166 * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
2169 protected void loadLastSavedBackupsOptions()
2171 BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
2172 .getSavedBackupEntry();
2173 enableBackupFiles.setSelected(
2174 Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
2176 BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
2177 .createBackupFilesPresetEntry(Cache
2178 .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
2179 if (backupfilesCustomEntry == null)
2181 backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2182 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
2184 BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
2185 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
2186 backupfilesCustomEntry);
2188 setComboIntStringKey(backupfilesPresetsCombo,
2189 Cache.getDefault(BackupFiles.NS + "_PRESET",
2190 BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
2192 backupsSetOptions(savedPreset);
2194 backupsOptionsSetEnabled();
2195 updateBackupFilesExampleLabel();
2198 private boolean warnAboutSuffixReverseChange()
2200 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
2201 .getSavedBackupEntry();
2202 boolean savedSuffixReverse = bfpe.reverse;
2203 int savedSuffixDigits = bfpe.digits;
2204 String savedSuffixTemplate = bfpe.suffix;
2206 boolean nowSuffixReverse = suffixReverse.isSelected();
2207 int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
2208 String nowSuffixTemplate = suffixTemplate.getText();
2209 return nowSuffixReverse != savedSuffixReverse
2210 && nowSuffixDigits == savedSuffixDigits
2211 && nowSuffixTemplate != null
2212 && nowSuffixTemplate.equals(savedSuffixTemplate);
2216 * Initialises the Backups tabbed panel.
2220 private JPanel initBackupsTab()
2222 JPanel backupsTab = new JPanel();
2223 backupsTab.setBorder(new TitledBorder(
2224 MessageManager.getString("label.backup_files")));
2225 backupsTab.setLayout(new GridBagLayout());
2227 GridBagConstraints gbc = new GridBagConstraints();
2230 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2231 gbc.fill = GridBagConstraints.NONE;
2233 initBackupsTabPresetsPanel();
2234 initBackupsTabSuffixPanel();
2235 initBackupsTabKeepFilesPanel();
2236 initBackupsTabFilenameExamplesPanel();
2238 enableBackupFiles.setFont(LABEL_FONT_BOLD);
2240 .setText(MessageManager.getString("label.enable_backupfiles"));
2241 enableBackupFiles.addActionListener(new ActionListener()
2244 public void actionPerformed(ActionEvent e)
2246 // enable other options only when the first is checked
2247 backupsOptionsSetEnabled();
2251 // enable checkbox 1 col
2255 gbc.gridy = 0; // row 0
2256 backupsTab.add(enableBackupFiles, gbc);
2258 // summary of scheme box (over two rows)
2262 gbc.anchor = GridBagConstraints.FIRST_LINE_END;
2263 gbc.fill = GridBagConstraints.BOTH;
2264 backupsTab.add(exampleFilesPanel, gbc);
2266 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2267 gbc.fill = GridBagConstraints.NONE;
2269 // fill empty space on right
2272 backupsTab.add(new JPanel(), gbc);
2277 gbc.gridy++; // row 1
2278 backupsTab.add(presetsPanel, gbc);
2280 // now using whole row
2285 gbc.gridy++; // row 2
2286 backupsTab.add(keepfilesPanel, gbc);
2288 // filename strategy box
2289 gbc.gridy++; // row 3
2290 backupsTab.add(suffixPanel, gbc);
2293 gbc.gridy++; // row 4
2295 backupsTab.add(new JPanel(), gbc);
2297 backupsOptionsSetEnabled();
2301 private JPanel initBackupsTabPresetsPanel()
2304 String title = MessageManager.getString("label.schemes");
2306 presetsPanel.setLayout(new GridBagLayout());
2308 GridBagConstraints gbc = new GridBagConstraints();
2311 gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2312 gbc.fill = GridBagConstraints.NONE;
2320 presetsComboLabel = new JLabel(title + ":");
2321 presetsPanel.add(presetsComboLabel, gbc);
2323 List<Object> entries = Arrays.asList(
2324 (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2325 List<String> tooltips = Arrays.asList(
2326 BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2327 backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2330 for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2332 backupfilesPresetsCombo
2333 .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2337 backupfilesPresetsCombo.addActionListener(new ActionListener()
2340 public void actionPerformed(ActionEvent e)
2342 int key = getComboIntStringKey(backupfilesPresetsCombo);
2343 if (!customiseCheckbox.isSelected())
2345 backupfilesPresetsComboLastSelected = key;
2347 if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2349 if (customiseCheckbox.isSelected())
2351 // got here by clicking on customiseCheckbox so don't change the
2353 backupfilesCustomOptionsSetEnabled();
2357 backupsTabUpdatePresets();
2358 backupfilesCustomOptionsSetEnabled();
2363 customiseCheckbox.setSelected(false);
2364 backupsTabUpdatePresets();
2365 backupfilesCustomOptionsSetEnabled();
2370 // dropdown list of preset schemes
2372 presetsPanel.add(backupfilesPresetsCombo, gbc);
2374 revertButton.setText(MessageManager.getString("label.cancel_changes"));
2375 revertButton.setToolTipText(
2376 MessageManager.getString("label.cancel_changes_description"));
2377 revertButton.addActionListener(new ActionListener()
2380 public void actionPerformed(ActionEvent e)
2383 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2384 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2385 backupfilesCustomOptionsSetEnabled();
2389 revertButton.setFont(LABEL_FONT);
2391 customiseCheckbox.setFont(LABEL_FONT);
2392 customiseCheckbox.setText(MessageManager.getString("label.customise"));
2393 customiseCheckbox.addActionListener(new ActionListener()
2396 public void actionPerformed(ActionEvent e)
2398 int currently = getComboIntStringKey(backupfilesPresetsCombo);
2399 if (customiseCheckbox.isSelected())
2401 backupfilesPresetsComboLastSelected = currently;
2402 setComboIntStringKey(backupfilesPresetsCombo,
2403 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2407 setComboIntStringKey(backupfilesPresetsCombo,
2408 backupfilesPresetsComboLastSelected);
2411 backupfilesCustomOptionsSetEnabled();
2414 customiseCheckbox.setToolTipText(
2415 MessageManager.getString("label.customise_description"));
2417 // customise checkbox
2420 presetsPanel.add(customiseCheckbox, gbc);
2422 // "Cancel changes" button (aligned with combo box above)
2424 presetsPanel.add(revertButton, gbc);
2426 return presetsPanel;
2429 private JPanel initBackupsTabFilenameExamplesPanel()
2431 String title = MessageManager.getString("label.scheme_examples");
2432 TitledBorder tb = new TitledBorder(title);
2433 exampleFilesPanel.setBorder(tb);
2434 exampleFilesPanel.setLayout(new GridBagLayout());
2436 backupfilesExampleLabel.setEditable(false);
2437 backupfilesExampleLabel
2438 .setBackground(exampleFilesPanel.getBackground());
2440 updateBackupFilesExampleLabel();
2442 GridBagConstraints gbc = new GridBagConstraints();
2445 gbc.fill = GridBagConstraints.NONE;
2446 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2448 exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2449 return exampleFilesPanel;
2452 private void backupsTabUpdatePresets()
2454 IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2457 String value = entry.v;
2459 if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2463 BackupFilesPresetEntry.backupfilesPresetEntriesValues
2469 "Preset '" + value + "' [key:" + key + "] not implemented");
2472 // Custom options will now be enabled when the customiseCheckbox is checked
2473 // (performed above)
2474 // backupfilesCustomOptionsSetEnabled();
2475 updateBackupFilesExampleLabel();
2478 protected int getComboIntStringKey(
2479 JComboBox<Object> backupfilesPresetsCombo2)
2481 IntKeyStringValueEntry e;
2484 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2486 } catch (Exception ex)
2489 "Problem casting Combo entry to IntKeyStringValueEntry.");
2492 return e != null ? e.k : 0;
2495 protected void setComboIntStringKey(
2496 JComboBox<Object> backupfilesPresetsCombo2, int key)
2498 for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2500 IntKeyStringValueEntry e;
2503 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2504 } catch (Exception ex)
2507 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2512 backupfilesPresetsCombo2.setSelectedIndex(i);
2516 // backupsTabUpdatePresets();
2519 private JPanel initBackupsTabSuffixPanel()
2521 suffixPanel.setBorder(new TitledBorder(
2522 MessageManager.getString("label.backup_filename_strategy")));
2523 suffixPanel.setLayout(new GridBagLayout());
2526 .setText(MessageManager.getString("label.append_to_filename"));
2527 suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2528 suffixTemplateLabel.setFont(LABEL_FONT);
2530 final String tooltip = JvSwingUtils.wrapTooltip(true,
2531 MessageManager.getString("label.append_to_filename_tooltip"));
2532 suffixTemplate.setToolTipText(tooltip);
2533 suffixTemplate.addActionListener(new ActionListener()
2536 public void actionPerformed(ActionEvent e)
2538 updateBackupFilesExampleLabel();
2539 backupfilesCustomOptionsSetEnabled();
2540 backupfilesRevertButtonSetEnabled(true);
2544 suffixTemplate.addKeyListener(new KeyListener()
2547 public void keyReleased(KeyEvent e)
2549 updateBackupFilesExampleLabel();
2550 backupfilesCustomOptionsSetEnabled();
2551 backupfilesRevertButtonSetEnabled(true);
2555 public void keyPressed(KeyEvent e)
2559 // disable use of ':' or '/' or '\'
2561 public void keyTyped(KeyEvent e)
2563 char c = e.getKeyChar();
2564 if (c == ':' || c == '/' || c == '\\')
2566 // don't process ':' or '/' or '\'
2575 .setText(MessageManager.getString("label.index_digits"));
2576 suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2577 suffixDigitsLabel.setFont(LABEL_FONT);
2578 ChangeListener c = new ChangeListener()
2581 public void stateChanged(ChangeEvent e)
2583 backupfilesRevertButtonSetEnabled(true);
2584 updateBackupFilesExampleLabel();
2588 setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2589 BackupFilesPresetEntry.DIGITSMAX, 3, c);
2591 suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2592 MessageManager.getString("label.increment_index"));
2593 suffixReverse.addActionListener(new ActionListener()
2596 public void actionPerformed(ActionEvent e)
2598 boolean okay = true;
2599 if (warnAboutSuffixReverseChange())
2602 okay = confirmSuffixReverseChange();
2606 backupfilesRevertButtonSetEnabled(true);
2607 updateBackupFilesExampleLabel();
2611 boolean savedSuffixReverse = BackupFilesPresetEntry
2612 .getSavedBackupEntry().reverse;
2613 suffixReverse.setSelected(savedSuffixReverse);
2618 GridBagConstraints sgbc = new GridBagConstraints();
2620 // first row (template text box)
2621 sgbc.anchor = GridBagConstraints.WEST;
2625 sgbc.gridheight = 1;
2628 sgbc.fill = GridBagConstraints.NONE;
2629 suffixPanel.add(suffixTemplateLabel, sgbc);
2632 sgbc.fill = GridBagConstraints.HORIZONTAL;
2633 suffixPanel.add(suffixTemplate, sgbc);
2635 // second row (number of digits spinner)
2639 sgbc.fill = GridBagConstraints.NONE;
2640 suffixPanel.add(suffixDigitsLabel, sgbc);
2643 sgbc.fill = GridBagConstraints.HORIZONTAL;
2644 suffixPanel.add(suffixDigitsSpinner, sgbc);
2646 // third row (forward order radio selection)
2649 sgbc.gridwidth = GridBagConstraints.REMAINDER;
2650 sgbc.fill = GridBagConstraints.HORIZONTAL;
2651 suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2653 // fourth row (reverse order radio selection)
2655 suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2659 private boolean confirmSuffixReverseChange()
2661 boolean ret = false;
2662 String warningMessage = MessageManager
2663 .getString("label.warning_confirm_change_reverse");
2664 int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2666 MessageManager.getString("label.change_increment_decrement"),
2667 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2669 ret = (confirm == JvOptionPane.YES_OPTION);
2673 private JPanel initBackupsTabKeepFilesPanel()
2675 keepfilesPanel.setBorder(
2676 new TitledBorder(MessageManager.getString("label.keep_files")));
2677 keepfilesPanel.setLayout(new GridBagLayout());
2679 backupfilesKeepAll.setLabels(
2680 MessageManager.getString("label.keep_all_backup_files"),
2681 MessageManager.getString(
2682 "label.keep_only_this_number_of_backup_files"));
2683 backupfilesKeepAll.addTrueActionListener(new ActionListener()
2686 public void actionPerformed(ActionEvent e)
2688 backupfilesRevertButtonSetEnabled(true);
2689 updateBackupFilesExampleLabel();
2692 backupfilesKeepAll.addActionListener(new ActionListener()
2695 public void actionPerformed(ActionEvent e)
2697 backupfilesRevertButtonSetEnabled(true);
2698 keepRollMaxOptionsEnabled();
2699 updateBackupFilesExampleLabel();
2703 ChangeListener c = new ChangeListener()
2706 public void stateChanged(ChangeEvent e)
2708 backupfilesRevertButtonSetEnabled(true);
2709 updateBackupFilesExampleLabel();
2713 setIntegerSpinner(backupfilesRollMaxSpinner,
2714 BackupFilesPresetEntry.ROLLMAXMIN,
2715 BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2717 backupfilesConfirmDelete.setLabels(
2718 MessageManager.getString("label.always_ask"),
2719 MessageManager.getString("label.auto_delete"));
2720 backupfilesConfirmDelete.addActionListener(new ActionListener()
2723 public void actionPerformed(ActionEvent e)
2725 backupfilesRevertButtonSetEnabled(true);
2728 // update the enabled section
2729 keepRollMaxOptionsEnabled();
2731 GridBagConstraints kgbc = new GridBagConstraints();
2733 // first row (template text box)
2734 kgbc.anchor = GridBagConstraints.WEST;
2737 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2738 kgbc.gridheight = 1;
2741 kgbc.fill = GridBagConstraints.HORIZONTAL;
2742 keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2748 kgbc.gridwidth = GridBagConstraints.RELATIVE;
2749 keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2752 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2753 keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2755 // third row (indented)
2757 kgbc.insets = new Insets(0, 20, 0, 0);
2760 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2761 kgbc.fill = GridBagConstraints.HORIZONTAL;
2764 JPanel jp = new JPanel();
2765 jp.setLayout(new FlowLayout());
2766 oldBackupFilesLabel.setText(
2767 MessageManager.getString("label.autodelete_old_backup_files"));
2768 oldBackupFilesLabel.setFont(LABEL_FONT);
2769 oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2770 jp.add(oldBackupFilesLabel);
2771 jp.add(backupfilesConfirmDelete.getTrueButton());
2772 jp.add(backupfilesConfirmDelete.getFalseButton());
2773 keepfilesPanel.add(jp, kgbc);
2775 return keepfilesPanel;
2778 protected void updateBackupFilesExampleLabel()
2780 int exampleindex = 12;
2781 String base = MessageManager.getString("label.filename") + ".fa";
2782 if (base == null || base.length() == 0)
2784 base = "file_name.fa";
2787 boolean reverse = suffixReverse.isSelected();
2788 boolean keepAll = backupfilesKeepAll.isSelected();
2790 String suffix = suffixTemplate.getText();
2793 backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2794 if (suffix == null || suffix.length() == 0)
2796 backupfilesExampleLabel
2797 .setText(MessageManager.getString("label.no_backup_files"));
2798 backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2802 rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2803 rollMax = rollMax < 1 ? 1 : rollMax;
2805 if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2810 digits = getSpinnerInt(suffixDigitsSpinner, 3);
2811 digits = digits < 1 ? 1 : digits;
2813 int lowersurround = 2;
2814 int uppersurround = 0;
2815 StringBuilder exampleSB = new StringBuilder();
2816 boolean firstLine = true;
2822 int max = keepAll ? exampleindex : rollMax;
2823 for (int index = min; index <= max; index++)
2825 if (index == min + lowersurround && index < max - uppersurround - 1)
2827 exampleSB.append("\n...");
2830 else if (index > min + lowersurround && index < max - uppersurround)
2842 exampleSB.append("\n");
2845 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2846 base, suffix, digits));
2849 // no extra text needed
2851 else if (index == min)
2853 String newest = MessageManager.getString("label.braced_newest");
2854 if (newest != null && newest.length() > 0)
2856 exampleSB.append(" " + newest);
2859 else if (index == max)
2861 String oldest = MessageManager.getString("label.braced_oldest");
2862 if (oldest != null && oldest.length() > 0)
2864 exampleSB.append(" " + oldest);
2873 int min = (keepAll || exampleindex - rollMax < 0) ? 1
2874 : exampleindex - rollMax + 1;
2875 int max = exampleindex;
2877 for (int index = min; index <= max; index++)
2880 if (index == min + lowersurround && index < max - uppersurround - 1)
2882 exampleSB.append("\n...");
2885 else if (index > min + lowersurround && index < max - uppersurround)
2897 exampleSB.append("\n");
2900 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2901 base, suffix, digits));
2904 // no extra text needed
2906 else if (index == min)
2908 String oldest = MessageManager.getString("label.braced_oldest");
2909 if (oldest != null && oldest.length() > 0)
2911 exampleSB.append(" " + oldest);
2914 else if (index == max)
2916 String newest = MessageManager.getString("label.braced_newest");
2917 if (newest != null && newest.length() > 0)
2919 exampleSB.append(" " + newest);
2927 // add some extra empty lines to pad out the example files box. ugh, please
2929 // me how to do this better
2930 int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2931 if (remainingLines > 0)
2933 for (int i = 0; i < remainingLines; i++)
2935 exampleSB.append("\n ");
2940 backupfilesExampleLabel.setText(exampleSB.toString());
2943 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2944 boolean useExistingVal, ChangeListener c)
2951 i = ((Integer) s.getValue()).intValue();
2952 } catch (Exception e)
2955 "Exception casting the initial value of s.getValue()");
2959 setIntegerSpinner(s, min, max, i, c);
2962 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2965 // integer spinner for number of digits
2974 SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2977 s.addChangeListener(c);
2981 protected static int getSpinnerInt(JSpinner s, int def)
2987 i = (Integer) s.getValue();
2988 } catch (Exception e)
2990 Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2995 private void keepRollMaxOptionsEnabled()
2997 boolean enabled = backupfilesKeepAll.isEnabled()
2998 && !backupfilesKeepAll.isSelected();
2999 oldBackupFilesLabel.setEnabled(enabled);
3000 backupfilesRollMaxSpinner.setEnabled(enabled);
3001 backupfilesConfirmDelete.setEnabled(enabled);
3004 private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
3006 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3007 && customiseCheckbox.isSelected() && suffixTemplate.getText()
3008 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
3009 keepfilesPanel.setEnabled(enabled);
3010 backupfilesKeepAll.setEnabled(enabled);
3011 oldBackupFilesLabel.setEnabled(enabled);
3012 keepRollMaxOptionsEnabled();
3015 private void backupfilesSuffixTemplateDigitsSetEnabled()
3017 boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
3018 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
3019 suffixDigitsLabel.setEnabled(enabled);
3020 suffixDigitsSpinner.setEnabled(enabled);
3021 suffixReverse.setEnabled(enabled);
3024 private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
3026 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3027 && customiseCheckbox.isSelected();
3028 suffixPanel.setEnabled(enabled);
3029 suffixTemplateLabel.setEnabled(enabled);
3030 suffixTemplate.setEnabled(enabled);
3031 backupfilesSuffixTemplateDigitsSetEnabled();
3034 private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
3036 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
3037 && customiseCheckbox.isSelected() && backupfilesCustomChanged();
3038 revertButton.setEnabled(enabled);
3041 private boolean backupfilesCustomChanged()
3043 BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
3044 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
3045 BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
3046 return !custom.equals(current);
3049 protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
3051 String suffix = suffixTemplate.getText();
3052 int digits = getSpinnerInt(suffixDigitsSpinner, 3);
3053 boolean reverse = suffixReverse.isSelected();
3054 boolean keepAll = backupfilesKeepAll.isSelected();
3055 int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
3056 boolean confirmDelete = backupfilesConfirmDelete.isSelected();
3058 BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
3059 reverse, keepAll, rollMax, confirmDelete);
3064 protected void backupfilesCustomOptionsSetEnabled()
3066 boolean enabled = customiseCheckbox.isSelected();
3068 backupfilesRevertButtonSetEnabled(enabled);
3069 backupfilesSuffixTemplateSetEnabled(enabled);
3070 backupfilesKeepAllSetEnabled(enabled);
3073 private void backupfilesSummarySetEnabled()
3075 boolean enabled = enableBackupFiles.isSelected();
3076 backupfilesExampleLabel.setEnabled(enabled);
3077 exampleFilesPanel.setEnabled(enabled);
3080 private void backupfilesPresetsSetEnabled()
3082 boolean enabled = enableBackupFiles.isSelected();
3083 presetsPanel.setEnabled(enabled);
3084 presetsComboLabel.setEnabled(enabled);
3085 backupfilesPresetsCombo.setEnabled(enabled);
3086 customiseCheckbox.setEnabled(enabled);
3087 revertButton.setEnabled(enabled);
3090 protected void backupsOptionsSetEnabled()
3092 backupfilesPresetsSetEnabled();
3093 backupfilesSummarySetEnabled();
3094 backupfilesCustomOptionsSetEnabled();
3097 protected void backupsSetOptions(String suffix, int digits,
3098 boolean reverse, boolean keepAll, int rollMax,
3099 boolean confirmDelete)
3101 suffixTemplate.setText(suffix);
3102 suffixDigitsSpinner.setValue(digits);
3103 suffixReverse.setSelected(reverse);
3104 backupfilesKeepAll.setSelected(keepAll);
3105 backupfilesRollMaxSpinner.setValue(rollMax);
3106 backupfilesConfirmDelete.setSelected(confirmDelete);
3109 protected void backupsSetOptions(BackupFilesPresetEntry p)
3111 backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
3115 protected void autoIdWidth_actionPerformed()
3117 // TODO Auto-generated method stub
3121 protected void userIdWidth_actionPerformed()
3123 // TODO Auto-generated method stub
3127 protected void maxColour_actionPerformed(JPanel panel)
3131 protected void minColour_actionPerformed(JPanel panel)
3135 protected void gapColour_actionPerformed(JPanel panel)
3139 protected void hiddenColour_actionPerformed(JPanel panel)
3143 protected void showunconserved_actionPerformed(ActionEvent e)
3145 // TODO Auto-generated method stub
3149 protected void useLegacyGaps_actionPerformed(ActionEvent e)
3153 protected void resetOvDefaults_actionPerformed(ActionEvent e)
3163 public void ok_actionPerformed(ActionEvent e)
3173 public void cancel_actionPerformed(ActionEvent e)
3183 public void annotations_actionPerformed(ActionEvent e)
3190 public void startupFileTextfield_mouseClicked()
3194 public void newLink_actionPerformed(ActionEvent e)
3199 public void editLink_actionPerformed(ActionEvent e)
3204 public void deleteLink_actionPerformed(ActionEvent e)
3209 public void defaultBrowser_mouseClicked(MouseEvent e)
3214 public void linkURLList_keyTyped(KeyEvent e)
3219 public void setProxyAuthEnabled()
3221 boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
3222 proxyAuthUsernameLabel.setEnabled(enabled);
3223 proxyAuthPasswordLabel.setEnabled(enabled);
3224 passwordNotStoredLabel.setEnabled(enabled);
3225 proxyAuthUsernameTB.setEnabled(enabled);
3226 proxyAuthPasswordPB.setEnabled(enabled);
3229 public void setCustomProxyEnabled()
3231 boolean enabled = customProxy.isSelected();
3232 portLabel.setEnabled(enabled);
3233 serverLabel.setEnabled(enabled);
3234 portLabel2.setEnabled(enabled);
3235 serverLabel2.setEnabled(enabled);
3236 httpLabel.setEnabled(enabled);
3237 httpsLabel.setEnabled(enabled);
3238 proxyServerHttpTB.setEnabled(enabled);
3239 proxyPortHttpTB.setEnabled(enabled);
3240 proxyServerHttpsTB.setEnabled(enabled);
3241 proxyPortHttpsTB.setEnabled(enabled);
3242 proxyAuth.setEnabled(enabled);
3243 setProxyAuthEnabled();
3246 public void proxyType_actionPerformed()
3248 setCustomProxyEnabled();
3249 proxyAuthPasswordCheckHighlight(true);
3250 applyProxyButtonEnabled(true);
3253 public void proxyAuth_actionPerformed()
3255 setProxyAuthEnabled();
3256 proxyAuthPasswordCheckHighlight(true);
3257 applyProxyButtonEnabled(true);
3261 * Customer renderer for JTable: supports column of radio buttons
3263 public class RadioButtonRenderer extends JRadioButton
3264 implements TableCellRenderer
3266 public RadioButtonRenderer()
3268 setHorizontalAlignment(CENTER);
3269 setToolTipText(MessageManager.getString("label.urltooltip"));
3273 public Component getTableCellRendererComponent(JTable table,
3274 Object value, boolean isSelected, boolean hasFocus, int row,
3277 setSelected((boolean) value);
3279 // set colours to match rest of table
3282 setBackground(table.getSelectionBackground());
3283 setForeground(table.getSelectionForeground());
3287 setBackground(table.getBackground());
3288 setForeground(table.getForeground());
3295 * Customer cell editor for JTable: supports column of radio buttons in
3296 * conjunction with renderer
3298 public class RadioButtonEditor extends AbstractCellEditor
3299 implements TableCellEditor
3301 private JRadioButton button = new JRadioButton();
3303 public RadioButtonEditor()
3305 button.setHorizontalAlignment(SwingConstants.CENTER);
3306 this.button.addActionListener(new ActionListener()
3309 public void actionPerformed(ActionEvent e)
3311 fireEditingStopped();
3317 public Component getTableCellEditorComponent(JTable table, Object value,
3318 boolean isSelected, int row, int column)
3320 button.setSelected((boolean) value);
3325 public Object getCellEditorValue()
3327 return button.isSelected();