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);
993 proxyAuthPasswordPB.setFont(LABEL_FONT);
994 proxyAuthPasswordPB.setColumns(30);
995 proxyAuthPasswordPB.getDocument()
996 .addDocumentListener(new DocumentListener()
999 public void changedUpdate(DocumentEvent e)
1001 proxyAuthPasswordHighlight(true);
1005 public void insertUpdate(DocumentEvent e)
1007 proxyAuthPasswordHighlight(true);
1011 public void removeUpdate(DocumentEvent e)
1013 proxyAuthPasswordHighlight(true);
1018 // Label for Port text box
1019 portLabel.setFont(LABEL_FONT);
1020 portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1021 portLabel.setText(MessageManager.getString("label.port") + ": ");
1022 portLabel2.setFont(LABEL_FONT);
1023 portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
1024 portLabel2.setText(MessageManager.getString("label.port") + ": ");
1026 httpLabel.setText("HTTP");
1027 httpLabel.setFont(LABEL_FONT_BOLD);
1028 httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
1029 httpsLabel.setText("HTTPS");
1030 httpsLabel.setFont(LABEL_FONT_BOLD);
1031 httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
1033 proxyAuthUsernameLabel
1034 .setText(MessageManager.getString("label.username") + ": ");
1035 proxyAuthUsernameLabel.setFont(LABEL_FONT);
1036 proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1037 proxyAuthPasswordLabel
1038 .setText(MessageManager.getString("label.password") + ": ");
1039 proxyAuthPasswordLabel.setFont(LABEL_FONT);
1040 proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1041 passwordNotStoredLabel.setText(
1042 "(" + MessageManager.getString("label.not_stored") + ")");
1043 passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
1044 passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
1046 // Proxy type radio buttons
1047 noProxy.setFont(LABEL_FONT);
1048 noProxy.setHorizontalAlignment(SwingConstants.LEFT);
1049 noProxy.setText(MessageManager.getString("label.no_proxy"));
1050 systemProxy.setFont(LABEL_FONT);
1051 systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
1052 systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
1053 displayUserHostPort(Cache.startupProxyProperties[4],
1054 Cache.startupProxyProperties[0],
1055 Cache.startupProxyProperties[1]),
1056 displayUserHostPort(Cache.startupProxyProperties[6],
1057 Cache.startupProxyProperties[2],
1058 Cache.startupProxyProperties[3])));
1059 customProxy.setFont(LABEL_FONT);
1060 customProxy.setHorizontalAlignment(SwingConstants.LEFT);
1061 customProxy.setText(
1062 MessageManager.getString("label.use_proxy_server") + ":");
1063 ActionListener al = new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 proxyType_actionPerformed();
1071 noProxy.addActionListener(al);
1072 systemProxy.addActionListener(al);
1073 customProxy.addActionListener(al);
1074 proxyType.add(noProxy);
1075 proxyType.add(systemProxy);
1076 proxyType.add(customProxy);
1078 proxyAuth.setFont(LABEL_FONT);
1079 proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
1080 proxyAuth.setText(MessageManager.getString("label.auth_required"));
1081 proxyAuth.addActionListener(new ActionListener()
1084 public void actionPerformed(ActionEvent e)
1086 proxyAuth_actionPerformed();
1090 setCustomProxyEnabled();
1092 // Make proxy server panel
1093 JPanel proxyPanel = new JPanel();
1094 TitledBorder titledBorder1 = new TitledBorder(
1095 MessageManager.getString("label.proxy_servers"));
1096 proxyPanel.setBorder(titledBorder1);
1097 proxyPanel.setLayout(new GridBagLayout());
1098 GridBagConstraints gbc = new GridBagConstraints();
1099 gbc.fill = GridBagConstraints.HORIZONTAL;
1102 GridBagConstraints c = new GridBagConstraints();
1103 // Proxy type radio buttons (3)
1104 JPanel ptPanel = new JPanel();
1105 ptPanel.setLayout(new GridBagLayout());
1110 c.fill = GridBagConstraints.HORIZONTAL;
1111 ptPanel.add(noProxy, c);
1113 ptPanel.add(systemProxy, c);
1115 ptPanel.add(customProxy, c);
1118 proxyPanel.add(ptPanel, gbc);
1120 // host and port text boxes
1121 JPanel hpPanel = new JPanel();
1122 hpPanel.setLayout(new GridBagLayout());
1123 // HTTP host port row
1128 c.anchor = GridBagConstraints.LINE_START;
1129 hpPanel.add(httpLabel, c);
1133 c.anchor = GridBagConstraints.LINE_END;
1134 hpPanel.add(serverLabel, c);
1138 c.anchor = GridBagConstraints.LINE_START;
1139 hpPanel.add(proxyServerHttpTB, c);
1143 c.anchor = GridBagConstraints.LINE_END;
1144 hpPanel.add(portLabel, c);
1148 c.anchor = GridBagConstraints.LINE_START;
1149 hpPanel.add(proxyPortHttpTB, c);
1151 // HTTPS host port row
1156 c.anchor = GridBagConstraints.LINE_START;
1157 hpPanel.add(httpsLabel, c);
1160 c.anchor = GridBagConstraints.LINE_END;
1161 hpPanel.add(serverLabel2, c);
1164 c.anchor = GridBagConstraints.LINE_START;
1165 hpPanel.add(proxyServerHttpsTB, c);
1168 c.anchor = GridBagConstraints.LINE_END;
1169 hpPanel.add(portLabel2, c);
1172 c.anchor = GridBagConstraints.LINE_START;
1173 hpPanel.add(proxyPortHttpsTB, c);
1176 proxyPanel.add(hpPanel, gbc);
1178 // Require authentication checkbox
1180 proxyPanel.add(proxyAuth, gbc);
1182 // username and password
1183 JPanel upPanel = new JPanel();
1184 upPanel.setLayout(new GridBagLayout());
1190 c.anchor = GridBagConstraints.LINE_END;
1191 upPanel.add(proxyAuthUsernameLabel, c);
1195 c.anchor = GridBagConstraints.LINE_START;
1196 upPanel.add(proxyAuthUsernameTB, c);
1202 c.anchor = GridBagConstraints.LINE_END;
1203 upPanel.add(proxyAuthPasswordLabel, c);
1207 c.anchor = GridBagConstraints.LINE_START;
1208 upPanel.add(proxyAuthPasswordPB, c);
1212 c.anchor = GridBagConstraints.LINE_START;
1213 upPanel.add(passwordNotStoredLabel, c);
1216 proxyPanel.add(upPanel, gbc);
1218 applyProxyButton.setText(MessageManager.getString("action.apply"));
1219 applyProxyButton.addActionListener(new ActionListener()
1222 public void actionPerformed(ActionEvent e)
1224 saveProxySettings();
1228 gbc.fill = GridBagConstraints.NONE;
1229 gbc.anchor = GridBagConstraints.LINE_END;
1230 proxyPanel.add(applyProxyButton, gbc);
1235 public void proxyAuthPasswordHighlight(boolean enabled)
1237 if (enabled && proxyType.isSelected(customProxy.getModel())
1238 && proxyAuth.isSelected()
1239 && !proxyAuthUsernameTB.getText().isEmpty()
1240 && proxyAuthPasswordPB.getDocument().getLength() == 0)
1243 proxyAuthPasswordPB.grabFocus();
1244 proxyAuthPasswordPB.setBackground(Color.PINK);
1248 proxyAuthPasswordPB.setBackground(Color.WHITE);
1252 public void saveProxySettings()
1254 // overridden in Preferences
1257 private String displayUserHostPort(String user, String host, String port)
1259 boolean hostBlank = (host == null || host.isEmpty());
1260 boolean portBlank = (port == null || port.isEmpty());
1261 if (hostBlank && portBlank)
1263 return MessageManager.getString("label.none");
1266 StringBuilder sb = new StringBuilder();
1269 sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
1273 sb.append(hostBlank ? "" : host);
1279 return sb.toString();
1283 * Initialises the checkboxes in the Connections tab
1285 private void initConnTabCheckboxes()
1287 // Usage stats checkbox label
1289 MessageManager.getString("label.send_usage_statistics"));
1290 usagestats.setFont(LABEL_FONT);
1291 usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
1292 usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
1294 // Questionnaire checkbox label
1295 questionnaire.setText(
1296 MessageManager.getString("label.check_for_questionnaires"));
1297 questionnaire.setFont(LABEL_FONT);
1298 questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
1299 questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
1301 // Check for latest version checkbox label
1302 versioncheck.setText(
1303 MessageManager.getString("label.check_for_latest_version"));
1304 versioncheck.setFont(LABEL_FONT);
1305 versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
1306 versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
1310 * Initialises the parent panel which contains the tabbed sections.
1314 private JPanel initOkCancelPanel()
1316 JButton ok = new JButton();
1317 ok.setText(MessageManager.getString("action.ok"));
1318 ok.addActionListener(new ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 ok_actionPerformed(e);
1326 JButton cancel = new JButton();
1327 cancel.setText(MessageManager.getString("action.cancel"));
1328 cancel.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 cancel_actionPerformed(e);
1336 JPanel okCancelPanel = new JPanel();
1337 okCancelPanel.add(ok);
1338 okCancelPanel.add(cancel);
1339 return okCancelPanel;
1343 * Initialises the Colours tabbed panel.
1347 private JPanel initColoursTab()
1349 JPanel coloursTab = new JPanel();
1350 coloursTab.setBorder(new TitledBorder(
1351 MessageManager.getString("action.open_new_alignment")));
1352 coloursTab.setLayout(new FlowLayout());
1353 JLabel mincolourLabel = new JLabel();
1354 mincolourLabel.setFont(LABEL_FONT);
1355 mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1356 mincolourLabel.setText(MessageManager.getString("label.min_colour"));
1357 minColour.setFont(LABEL_FONT);
1358 minColour.setBorder(BorderFactory.createEtchedBorder());
1359 minColour.setPreferredSize(new Dimension(40, 20));
1360 minColour.addMouseListener(new MouseAdapter()
1363 public void mousePressed(MouseEvent e)
1365 minColour_actionPerformed(minColour);
1368 JLabel maxcolourLabel = new JLabel();
1369 maxcolourLabel.setFont(LABEL_FONT);
1370 maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1371 maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
1372 maxColour.setFont(LABEL_FONT);
1373 maxColour.setBorder(BorderFactory.createEtchedBorder());
1374 maxColour.setPreferredSize(new Dimension(40, 20));
1375 maxColour.addMouseListener(new MouseAdapter()
1378 public void mousePressed(MouseEvent e)
1380 maxColour_actionPerformed(maxColour);
1384 protColour.setFont(LABEL_FONT);
1385 protColour.setBounds(new Rectangle(172, 225, 155, 21));
1386 JLabel protColourLabel = new JLabel();
1387 protColourLabel.setFont(LABEL_FONT);
1388 protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1389 protColourLabel.setText(
1390 MessageManager.getString("label.prot_alignment_colour") + " ");
1391 JvSwingUtils.addtoLayout(coloursTab,
1393 .getString("label.default_colour_scheme_for_alignment"),
1394 protColourLabel, protColour);
1396 nucColour.setFont(LABEL_FONT);
1397 nucColour.setBounds(new Rectangle(172, 240, 155, 21));
1398 JLabel nucColourLabel = new JLabel();
1399 nucColourLabel.setFont(LABEL_FONT);
1400 nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
1401 nucColourLabel.setText(
1402 MessageManager.getString("label.nuc_alignment_colour") + " ");
1403 JvSwingUtils.addtoLayout(coloursTab,
1405 .getString("label.default_colour_scheme_for_alignment"),
1406 nucColourLabel, nucColour);
1408 JPanel annotationShding = new JPanel();
1409 annotationShding.setBorder(new TitledBorder(
1410 MessageManager.getString("label.annotation_shading_default")));
1411 annotationShding.setLayout(new GridLayout(1, 2));
1412 JvSwingUtils.addtoLayout(annotationShding,
1413 MessageManager.getString(
1414 "label.default_minimum_colour_annotation_shading"),
1415 mincolourLabel, minColour);
1416 JvSwingUtils.addtoLayout(annotationShding,
1417 MessageManager.getString(
1418 "label.default_maximum_colour_annotation_shading"),
1419 maxcolourLabel, maxColour);
1420 coloursTab.add(annotationShding); // , FlowLayout.LEFT);
1425 * Initialises the Overview tabbed panel.
1429 private JPanel initOverviewTab()
1431 JPanel overviewPanel = new JPanel();
1432 overviewPanel.setBorder(new TitledBorder(
1433 MessageManager.getString("label.overview_settings")));
1435 gapColour.setFont(LABEL_FONT);
1436 // fixing the border colours stops apparent colour bleed from the panel
1437 gapColour.setBorder(
1438 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1439 gapColour.setPreferredSize(new Dimension(40, 20));
1440 gapColour.addMouseListener(new MouseAdapter()
1443 public void mousePressed(MouseEvent e)
1445 gapColour_actionPerformed(gapColour);
1449 hiddenColour.setFont(LABEL_FONT);
1450 // fixing the border colours stops apparent colour bleed from the panel
1451 hiddenColour.setBorder(
1452 BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
1453 hiddenColour.setPreferredSize(new Dimension(40, 20));
1454 hiddenColour.addMouseListener(new MouseAdapter()
1457 public void mousePressed(MouseEvent e)
1459 hiddenColour_actionPerformed(hiddenColour);
1463 useLegacyGap = new JCheckBox(
1464 MessageManager.getString("label.ov_legacy_gap"));
1465 useLegacyGap.setFont(LABEL_FONT);
1466 useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
1467 useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
1468 gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
1469 gapLabel.setFont(LABEL_FONT);
1470 gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
1471 gapLabel.setVerticalTextPosition(SwingConstants.TOP);
1472 showHiddenAtStart = new JCheckBox(
1473 MessageManager.getString("label.ov_show_hide_default"));
1474 showHiddenAtStart.setFont(LABEL_FONT);
1475 showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
1476 showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
1477 JLabel hiddenLabel = new JLabel(
1478 MessageManager.getString("label.hidden_colour"));
1479 hiddenLabel.setFont(LABEL_FONT);
1480 hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
1481 hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
1483 useLegacyGap.addActionListener(new ActionListener()
1486 public void actionPerformed(ActionEvent e)
1488 useLegacyGaps_actionPerformed(e);
1492 overviewPanel.setLayout(new GridBagLayout());
1493 GridBagConstraints c1 = new GridBagConstraints();
1495 c1.fill = GridBagConstraints.HORIZONTAL;
1500 c1.anchor = GridBagConstraints.FIRST_LINE_START;
1501 overviewPanel.add(useLegacyGap, c1);
1503 GridBagConstraints c2 = new GridBagConstraints();
1504 c2.fill = GridBagConstraints.HORIZONTAL;
1507 c2.insets = new Insets(0, 15, 0, 10);
1508 overviewPanel.add(gapLabel, c2);
1510 GridBagConstraints c3 = new GridBagConstraints();
1511 c3.fill = GridBagConstraints.HORIZONTAL;
1514 c3.insets = new Insets(0, 0, 0, 15);
1515 overviewPanel.add(gapColour, c3);
1517 GridBagConstraints c4 = new GridBagConstraints();
1518 c4.fill = GridBagConstraints.HORIZONTAL;
1522 overviewPanel.add(showHiddenAtStart, c4);
1524 GridBagConstraints c5 = new GridBagConstraints();
1525 c5.fill = GridBagConstraints.HORIZONTAL;
1528 c5.insets = new Insets(0, 15, 0, 10);
1529 overviewPanel.add(hiddenLabel, c5);
1531 GridBagConstraints c6 = new GridBagConstraints();
1532 c6.fill = GridBagConstraints.HORIZONTAL;
1535 c6.insets = new Insets(0, 0, 0, 15);
1536 overviewPanel.add(hiddenColour, c6);
1538 JButton resetButton = new JButton(
1539 MessageManager.getString("label.reset_to_defaults"));
1541 resetButton.addActionListener(new ActionListener()
1544 public void actionPerformed(ActionEvent e)
1546 resetOvDefaults_actionPerformed(e);
1550 GridBagConstraints c7 = new GridBagConstraints();
1551 c7.fill = GridBagConstraints.NONE;
1554 c7.insets = new Insets(10, 0, 0, 0);
1555 c7.anchor = GridBagConstraints.WEST;
1556 overviewPanel.add(resetButton, c7);
1558 // Add padding so the panel doesn't look ridiculous
1559 JPanel spacePanel = new JPanel();
1560 overviewPanel.add(spacePanel,
1561 new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
1562 GridBagConstraints.WEST, GridBagConstraints.BOTH,
1563 new Insets(0, 0, 0, 5), 0, 0));
1565 return overviewPanel;
1569 * Initialises the Structure tabbed panel.
1573 private JPanel initStructureTab()
1575 structureTab = new JPanel();
1577 structureTab.setBorder(new TitledBorder(
1578 MessageManager.getString("label.structure_options")));
1579 structureTab.setLayout(null);
1580 final int width = 420;
1581 final int height = 22;
1582 final int lineSpacing = 25;
1585 structFromPdb.setFont(LABEL_FONT);
1587 .setText(MessageManager.getString("label.struct_from_pdb"));
1588 structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
1589 structFromPdb.addActionListener(new ActionListener()
1592 public void actionPerformed(ActionEvent e)
1594 boolean selected = structFromPdb.isSelected();
1595 // enable other options only when the first is checked
1596 useRnaView.setEnabled(selected);
1597 addSecondaryStructure.setEnabled(selected);
1598 addTempFactor.setEnabled(selected);
1601 structureTab.add(structFromPdb);
1603 // indent checkboxes that are conditional on the first one
1604 ypos += lineSpacing;
1605 useRnaView.setFont(LABEL_FONT);
1606 useRnaView.setText(MessageManager.getString("label.use_rnaview"));
1607 useRnaView.setBounds(new Rectangle(25, ypos, width, height));
1608 structureTab.add(useRnaView);
1610 ypos += lineSpacing;
1611 addSecondaryStructure.setFont(LABEL_FONT);
1612 addSecondaryStructure
1613 .setText(MessageManager.getString("label.autoadd_secstr"));
1614 addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1615 structureTab.add(addSecondaryStructure);
1617 ypos += lineSpacing;
1618 addTempFactor.setFont(LABEL_FONT);
1619 addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1620 addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1621 structureTab.add(addTempFactor);
1623 ypos += lineSpacing;
1624 JLabel viewerLabel = new JLabel();
1625 viewerLabel.setFont(LABEL_FONT);
1626 viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1627 viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1628 viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
1629 structureTab.add(viewerLabel);
1632 * add all external viewers as options here - check
1633 * when selected whether the program is installed
1635 structViewer.setFont(LABEL_FONT);
1636 structViewer.setBounds(new Rectangle(190, ypos, 120, height));
1637 structViewer.addItem(ViewerType.JMOL.name());
1638 structViewer.addItem(ViewerType.CHIMERA.name());
1639 structViewer.addItem(ViewerType.CHIMERAX.name());
1640 structViewer.addItem(ViewerType.PYMOL.name());
1641 structViewer.addActionListener(new ActionListener()
1644 public void actionPerformed(ActionEvent e)
1646 structureViewer_actionPerformed(
1647 (String) structViewer.getSelectedItem());
1650 structureTab.add(structViewer);
1652 ypos += lineSpacing;
1653 structureViewerPathLabel = new JLabel();
1654 structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11));
1655 structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1656 structureViewerPathLabel.setText(MessageManager
1657 .formatMessage("label.viewer_path", "Chimera(X)"));
1658 structureViewerPathLabel.setBounds(new Rectangle(10, ypos, 170, height));
1659 structureViewerPathLabel.setEnabled(false);
1660 structureTab.add(structureViewerPathLabel);
1662 structureViewerPath.setFont(LABEL_FONT);
1663 structureViewerPath.setText("");
1664 structureViewerPath.setEnabled(false);
1665 final String tooltip = JvSwingUtils.wrapTooltip(true,
1666 MessageManager.getString("label.viewer_path_tip"));
1667 structureViewerPath.setToolTipText(tooltip);
1668 structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
1669 structureViewerPath.addMouseListener(new MouseAdapter()
1672 public void mouseClicked(MouseEvent e)
1674 if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
1676 String chosen = openFileChooser();
1679 structureViewerPath.setText(chosen);
1684 structureTab.add(structureViewerPath);
1686 ypos += lineSpacing;
1687 nwMapping.setFont(LABEL_FONT);
1688 nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1689 siftsMapping.setFont(LABEL_FONT);
1690 siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1691 mappingMethod.add(nwMapping);
1692 mappingMethod.add(siftsMapping);
1693 JPanel mappingPanel = new JPanel();
1694 mappingPanel.setFont(LABEL_FONT);
1695 TitledBorder mmTitledBorder = new TitledBorder(
1696 MessageManager.getString("label.mapping_method"));
1697 mmTitledBorder.setTitleFont(LABEL_FONT);
1698 mappingPanel.setBorder(mmTitledBorder);
1699 mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
1700 // GridLayout mappingLayout = new GridLayout();
1701 mappingPanel.setLayout(new GridLayout());
1702 mappingPanel.add(nwMapping);
1703 mappingPanel.add(siftsMapping);
1704 structureTab.add(mappingPanel);
1706 ypos += lineSpacing;
1707 ypos += lineSpacing;
1708 FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1709 PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1710 docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
1711 structureTab.add(docFieldPref);
1714 * hide Chimera options in JalviewJS
1716 if (Platform.isJS())
1718 structureViewerPathLabel.setVisible(false);
1719 structureViewerPath.setVisible(false);
1720 viewerLabel.setVisible(false);
1721 structViewer.setVisible(false);
1724 return structureTab;
1728 * Action on choosing a structure viewer from combobox options.
1730 * @param selectedItem
1732 protected void structureViewer_actionPerformed(String selectedItem)
1737 * Show a dialog for the user to choose a file. Returns the chosen path, or
1742 protected String openFileChooser()
1744 String choice = null;
1745 JFileChooser chooser = new JFileChooser();
1747 // chooser.setFileView(new JalviewFileView());
1748 chooser.setDialogTitle(
1749 MessageManager.getString("label.open_local_file"));
1750 chooser.setToolTipText(MessageManager.getString("action.open"));
1752 int value = chooser.showOpenDialog(this);
1754 if (value == JFileChooser.APPROVE_OPTION)
1756 choice = chooser.getSelectedFile().getPath();
1762 * Validate the structure tab preferences; if invalid, set focus on this tab.
1766 protected boolean validateStructure(FocusEvent e)
1768 if (!validateStructure())
1770 e.getComponent().requestFocusInWindow();
1776 protected boolean validateStructure()
1782 * Initialises the Visual tabbed panel.
1786 private JPanel initVisualTab()
1788 JPanel visualTab = new JPanel();
1789 visualTab.setBorder(new TitledBorder(
1790 MessageManager.getString("action.open_new_alignment")));
1791 visualTab.setLayout(null);
1792 fullScreen.setFont(LABEL_FONT);
1793 fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1794 fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1795 fullScreen.setText(MessageManager.getString("label.maximize_window"));
1796 quality.setEnabled(false);
1797 quality.setFont(LABEL_FONT);
1798 quality.setHorizontalAlignment(SwingConstants.RIGHT);
1799 quality.setHorizontalTextPosition(SwingConstants.LEFT);
1800 quality.setSelected(true);
1801 quality.setText(MessageManager.getString("label.quality"));
1802 conservation.setEnabled(false);
1803 conservation.setFont(LABEL_FONT);
1804 conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1805 conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1806 conservation.setSelected(true);
1807 conservation.setText(MessageManager.getString("label.conservation"));
1808 identity.setEnabled(false);
1809 identity.setFont(LABEL_FONT);
1810 identity.setHorizontalAlignment(SwingConstants.RIGHT);
1811 identity.setHorizontalTextPosition(SwingConstants.LEFT);
1812 identity.setSelected(true);
1813 identity.setText(MessageManager.getString("label.consensus"));
1814 showOccupancy.setFont(LABEL_FONT);
1815 showOccupancy.setEnabled(false);
1816 showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1817 showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1818 showOccupancy.setSelected(true);
1819 showOccupancy.setText(MessageManager.getString("label.occupancy"));
1821 JLabel showGroupbits = new JLabel();
1822 showGroupbits.setFont(LABEL_FONT);
1823 showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1824 showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1826 .setText(MessageManager.getString("action.show_group") + ":");
1827 JLabel showConsensbits = new JLabel();
1828 showConsensbits.setFont(LABEL_FONT);
1829 showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1830 showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1832 .setText(MessageManager.getString("label.consensus") + ":");
1833 showConsensHistogram.setEnabled(false);
1834 showConsensHistogram.setFont(LABEL_FONT);
1835 showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1836 showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1837 showConsensHistogram.setSelected(true);
1838 showConsensHistogram
1839 .setText(MessageManager.getString("label.histogram"));
1840 showConsensLogo.setEnabled(false);
1841 showConsensLogo.setFont(LABEL_FONT);
1842 showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1843 showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1844 showConsensLogo.setSelected(true);
1845 showConsensLogo.setText(MessageManager.getString("label.logo"));
1846 showGroupConsensus.setEnabled(false);
1847 showGroupConsensus.setFont(LABEL_FONT);
1848 showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1849 showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1850 showGroupConsensus.setSelected(true);
1851 showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1852 showGroupConservation.setEnabled(false);
1853 showGroupConservation.setFont(LABEL_FONT);
1854 showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1855 showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1856 showGroupConservation.setSelected(true);
1857 showGroupConservation
1858 .setText(MessageManager.getString("label.conservation"));
1859 showNpTooltip.setEnabled(true);
1860 showNpTooltip.setFont(LABEL_FONT);
1861 showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1862 showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1863 showNpTooltip.setSelected(true);
1864 showNpTooltip.setText(
1865 MessageManager.getString("label.non_positional_features"));
1866 showDbRefTooltip.setEnabled(true);
1867 showDbRefTooltip.setFont(LABEL_FONT);
1868 showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1869 showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1870 showDbRefTooltip.setSelected(true);
1872 .setText(MessageManager.getString("label.database_references"));
1873 annotations.setFont(LABEL_FONT);
1874 annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1875 annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1876 annotations.setSelected(true);
1877 annotations.setText(MessageManager.getString("label.show_annotations"));
1878 // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1879 annotations.addActionListener(new ActionListener()
1882 public void actionPerformed(ActionEvent e)
1884 annotations_actionPerformed(e);
1887 identity.addActionListener(new ActionListener()
1890 public void actionPerformed(ActionEvent e)
1892 annotations_actionPerformed(e);
1895 showGroupConsensus.addActionListener(new ActionListener()
1898 public void actionPerformed(ActionEvent e)
1900 annotations_actionPerformed(e);
1903 showUnconserved.setFont(LABEL_FONT);
1904 showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1905 showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1906 showUnconserved.setSelected(true);
1908 .setText(MessageManager.getString("action.show_unconserved"));
1909 showUnconserved.addActionListener(new ActionListener()
1912 public void actionPerformed(ActionEvent e)
1914 showunconserved_actionPerformed(e);
1918 // TODO these are not yet added to / action from Preferences
1919 // JCheckBox shareSelections = new JCheckBox();
1920 // shareSelections.setFont(verdana11);
1921 // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1922 // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1923 // shareSelections.setSelected(true);
1924 // shareSelections.setText(MessageManager
1925 // .getString("label.share_selection_across_views"));
1926 // JCheckBox followHighlight = new JCheckBox();
1927 // followHighlight.setFont(verdana11);
1928 // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1929 // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1930 // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1931 // followHighlight.setSelected(true);
1932 // followHighlight.setText(MessageManager
1933 // .getString("label.scroll_highlighted_regions"));
1935 seqLimit.setFont(LABEL_FONT);
1936 seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1937 seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1938 seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1939 smoothFont.setFont(LABEL_FONT);
1940 smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1941 smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1942 smoothFont.setText(MessageManager.getString("label.smooth_font"));
1943 scaleProteinToCdna.setFont(LABEL_FONT);
1944 scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1945 scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1946 scaleProteinToCdna.setText(
1947 MessageManager.getString("label.scale_protein_to_cdna"));
1948 scaleProteinToCdna.setToolTipText(
1949 MessageManager.getString("label.scale_protein_to_cdna_tip"));
1950 JLabel gapLabel = new JLabel();
1951 gapLabel.setFont(LABEL_FONT);
1952 gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1953 gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1954 JLabel fontLabel = new JLabel();
1955 fontLabel.setFont(LABEL_FONT);
1956 fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1957 fontLabel.setText(MessageManager.getString("label.font"));
1958 fontSizeCB.setFont(LABEL_FONT);
1959 fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1960 fontStyleCB.setFont(LABEL_FONT);
1961 fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1962 fontNameCB.setFont(LABEL_FONT);
1963 fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1964 gapSymbolCB.setFont(LABEL_FONT);
1965 gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1966 DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1967 dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1968 gapSymbolCB.setRenderer(dlcr);
1970 startupCheckbox.setText(MessageManager.getString("action.open_file"));
1971 startupCheckbox.setFont(LABEL_FONT);
1972 startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1973 startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1974 startupCheckbox.setSelected(true);
1975 startupFileTextfield.setFont(LABEL_FONT);
1976 startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1977 final String tooltip = JvSwingUtils.wrapTooltip(true,
1978 MessageManager.getString("label.double_click_to_browse"));
1979 startupFileTextfield.setToolTipText(tooltip);
1980 startupFileTextfield.addMouseListener(new MouseAdapter()
1983 public void mouseClicked(MouseEvent e)
1985 if (e.getClickCount() > 1)
1987 startupFileTextfield_mouseClicked();
1992 sortby.setFont(LABEL_FONT);
1993 sortby.setBounds(new Rectangle(172, 260, 155, 21));
1994 JLabel sortLabel = new JLabel();
1995 sortLabel.setFont(LABEL_FONT);
1996 sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1997 sortLabel.setText(MessageManager.getString("label.sort_by"));
1998 sortAnnBy.setFont(LABEL_FONT);
1999 sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
2000 JLabel sortAnnLabel = new JLabel();
2001 sortAnnLabel.setFont(LABEL_FONT);
2002 sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
2003 sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
2004 sortAutocalc.setFont(LABEL_FONT);
2005 sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
2007 JPanel annsettingsPanel = new JPanel();
2008 annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
2009 annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
2010 annsettingsPanel.setBorder(new EtchedBorder());
2011 visualTab.add(annsettingsPanel);
2012 Border jb = new EmptyBorder(1, 1, 4, 5);
2013 annotations.setBorder(jb);
2014 showOccupancy.setBorder(jb);
2015 quality.setBorder(jb);
2016 conservation.setBorder(jb);
2017 identity.setBorder(jb);
2018 showConsensbits.setBorder(jb);
2019 showGroupbits.setBorder(jb);
2020 showGroupConsensus.setBorder(jb);
2021 showGroupConservation.setBorder(jb);
2022 showConsensHistogram.setBorder(jb);
2023 showConsensLogo.setBorder(jb);
2025 JPanel autoAnnotSettings = new JPanel();
2026 annsettingsPanel.add(autoAnnotSettings);
2027 autoAnnotSettings.setLayout(new GridLayout(0, 2));
2028 autoAnnotSettings.add(annotations);
2029 autoAnnotSettings.add(quality);
2030 // second row of autoannotation box
2031 autoAnnotSettings = new JPanel();
2032 annsettingsPanel.add(autoAnnotSettings);
2034 autoAnnotSettings.setLayout(new GridLayout(0, 3));
2035 autoAnnotSettings.add(conservation);
2036 autoAnnotSettings.add(identity);
2037 autoAnnotSettings.add(showOccupancy);
2038 autoAnnotSettings.add(showGroupbits);
2039 autoAnnotSettings.add(showGroupConservation);
2040 autoAnnotSettings.add(showGroupConsensus);
2041 autoAnnotSettings.add(showConsensbits);
2042 autoAnnotSettings.add(showConsensHistogram);
2043 autoAnnotSettings.add(showConsensLogo);
2045 JPanel tooltipSettings = new JPanel();
2046 tooltipSettings.setBorder(new TitledBorder(
2047 MessageManager.getString("label.sequence_id_tooltip")));
2048 tooltipSettings.setBounds(173, 140, 220, 62);
2049 tooltipSettings.setLayout(new GridLayout(2, 1));
2050 tooltipSettings.add(showDbRefTooltip);
2051 tooltipSettings.add(showNpTooltip);
2052 visualTab.add(tooltipSettings);
2054 wrap.setFont(LABEL_FONT);
2055 wrap.setHorizontalAlignment(SwingConstants.TRAILING);
2056 wrap.setHorizontalTextPosition(SwingConstants.LEADING);
2057 wrap.setText(MessageManager.getString("label.wrap_alignment"));
2058 rightAlign.setFont(LABEL_FONT);
2059 rightAlign.setForeground(Color.black);
2060 rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
2061 rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
2062 rightAlign.setText(MessageManager.getString("label.right_align_ids"));
2063 idItalics.setFont(LABEL_FONT_ITALIC);
2064 idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
2065 idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
2067 MessageManager.getString("label.sequence_name_italics"));
2068 openoverv.setFont(LABEL_FONT);
2069 openoverv.setActionCommand(
2070 MessageManager.getString("label.open_overview"));
2071 openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
2072 openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
2073 openoverv.setText(MessageManager.getString("label.open_overview"));
2074 JPanel jPanel2 = new JPanel();
2075 jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
2076 jPanel2.setLayout(new GridLayout(14, 1));
2077 jPanel2.add(fullScreen);
2078 jPanel2.add(openoverv);
2079 jPanel2.add(seqLimit);
2080 jPanel2.add(rightAlign);
2081 jPanel2.add(fontLabel);
2082 jPanel2.add(showUnconserved);
2083 jPanel2.add(idItalics);
2084 jPanel2.add(smoothFont);
2085 jPanel2.add(scaleProteinToCdna);
2086 jPanel2.add(gapLabel);
2088 jPanel2.add(sortLabel);
2089 jPanel2.add(sortAnnLabel);
2090 jPanel2.add(startupCheckbox);
2091 visualTab.add(jPanel2);
2092 visualTab.add(startupFileTextfield);
2093 visualTab.add(sortby);
2094 visualTab.add(sortAnnBy);
2095 visualTab.add(sortAutocalc);
2096 visualTab.add(gapSymbolCB);
2097 visualTab.add(fontNameCB);
2098 visualTab.add(fontSizeCB);
2099 visualTab.add(fontStyleCB);
2101 if (Platform.isJS())
2103 startupCheckbox.setVisible(false);
2104 startupFileTextfield.setVisible(false);
2111 * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
2114 protected void loadLastSavedBackupsOptions()
2116 BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
2117 .getSavedBackupEntry();
2119 .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
2121 BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
2122 .createBackupFilesPresetEntry(Cache
2123 .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
2124 if (backupfilesCustomEntry == null)
2126 backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2127 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
2129 BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
2130 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
2131 backupfilesCustomEntry);
2133 setComboIntStringKey(backupfilesPresetsCombo,
2134 Cache.getDefault(BackupFiles.NS + "_PRESET",
2135 BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
2137 backupsSetOptions(savedPreset);
2139 backupsOptionsSetEnabled();
2140 updateBackupFilesExampleLabel();
2143 private boolean warnAboutSuffixReverseChange()
2145 BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
2146 .getSavedBackupEntry();
2147 boolean savedSuffixReverse = bfpe.reverse;
2148 int savedSuffixDigits = bfpe.digits;
2149 String savedSuffixTemplate = bfpe.suffix;
2151 boolean nowSuffixReverse = suffixReverse.isSelected();
2152 int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
2153 String nowSuffixTemplate = suffixTemplate.getText();
2154 return nowSuffixReverse != savedSuffixReverse
2155 && nowSuffixDigits == savedSuffixDigits
2156 && nowSuffixTemplate != null
2157 && nowSuffixTemplate.equals(savedSuffixTemplate);
2161 * Initialises the Backups tabbed panel.
2165 private JPanel initBackupsTab()
2167 JPanel backupsTab = new JPanel();
2168 backupsTab.setBorder(new TitledBorder(
2169 MessageManager.getString("label.backup_files")));
2170 backupsTab.setLayout(new GridBagLayout());
2172 GridBagConstraints gbc = new GridBagConstraints();
2175 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2176 gbc.fill = GridBagConstraints.NONE;
2178 initBackupsTabPresetsPanel();
2179 initBackupsTabSuffixPanel();
2180 initBackupsTabKeepFilesPanel();
2181 initBackupsTabFilenameExamplesPanel();
2183 enableBackupFiles.setFont(LABEL_FONT_BOLD);
2185 .setText(MessageManager.getString("label.enable_backupfiles"));
2186 enableBackupFiles.addActionListener(new ActionListener()
2189 public void actionPerformed(ActionEvent e)
2191 // enable other options only when the first is checked
2192 backupsOptionsSetEnabled();
2197 // enable checkbox 1 col
2201 gbc.gridy = 0; // row 0
2202 backupsTab.add(enableBackupFiles, gbc);
2204 // summary of scheme box (over two rows)
2208 gbc.anchor = GridBagConstraints.FIRST_LINE_END;
2209 gbc.fill = GridBagConstraints.BOTH;
2210 backupsTab.add(exampleFilesPanel, gbc);
2212 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2213 gbc.fill = GridBagConstraints.NONE;
2215 // fill empty space on right
2218 backupsTab.add(new JPanel(), gbc);
2223 gbc.gridy++; // row 1
2224 backupsTab.add(presetsPanel, gbc);
2226 // now using whole row
2231 gbc.gridy++; // row 2
2232 backupsTab.add(keepfilesPanel, gbc);
2234 // filename strategy box
2235 gbc.gridy++; // row 3
2236 backupsTab.add(suffixPanel, gbc);
2239 gbc.gridy++; // row 4
2241 backupsTab.add(new JPanel(), gbc);
2243 backupsOptionsSetEnabled();
2247 private JPanel initBackupsTabPresetsPanel()
2250 String title = MessageManager.getString("label.schemes");
2252 presetsPanel.setLayout(new GridBagLayout());
2254 GridBagConstraints gbc = new GridBagConstraints();
2257 gbc.anchor = GridBagConstraints.BASELINE_LEADING;
2258 gbc.fill = GridBagConstraints.NONE;
2266 presetsComboLabel = new JLabel(title + ":");
2267 presetsPanel.add(presetsComboLabel, gbc);
2269 List<Object> entries = Arrays
2270 .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
2271 List<String> tooltips = Arrays.asList(
2272 BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
2273 backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
2276 for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
2278 backupfilesPresetsCombo
2279 .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
2283 backupfilesPresetsCombo.addActionListener(new ActionListener()
2286 public void actionPerformed(ActionEvent e)
2288 int key = getComboIntStringKey(backupfilesPresetsCombo);
2289 if (!customiseCheckbox.isSelected())
2291 backupfilesPresetsComboLastSelected = key;
2293 if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
2295 if (customiseCheckbox.isSelected())
2297 // got here by clicking on customiseCheckbox so don't change the values
2298 backupfilesCustomOptionsSetEnabled();
2302 backupsTabUpdatePresets();
2303 backupfilesCustomOptionsSetEnabled();
2308 customiseCheckbox.setSelected(false);
2309 backupsTabUpdatePresets();
2310 backupfilesCustomOptionsSetEnabled();
2315 // dropdown list of preset schemes
2317 presetsPanel.add(backupfilesPresetsCombo, gbc);
2319 revertButton.setText(MessageManager.getString("label.cancel_changes"));
2320 revertButton.setToolTipText(
2321 MessageManager.getString("label.cancel_changes_description"));
2322 revertButton.addActionListener(new ActionListener()
2325 public void actionPerformed(ActionEvent e)
2328 BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
2329 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
2330 backupfilesCustomOptionsSetEnabled();
2334 revertButton.setFont(LABEL_FONT);
2336 customiseCheckbox.setFont(LABEL_FONT);
2337 customiseCheckbox.setText(MessageManager.getString("label.customise"));
2338 customiseCheckbox.addActionListener(new ActionListener()
2341 public void actionPerformed(ActionEvent e)
2343 int currently = getComboIntStringKey(backupfilesPresetsCombo);
2344 if (customiseCheckbox.isSelected())
2346 backupfilesPresetsComboLastSelected = currently;
2347 setComboIntStringKey(backupfilesPresetsCombo,
2348 BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2352 setComboIntStringKey(backupfilesPresetsCombo,
2353 backupfilesPresetsComboLastSelected);
2356 backupfilesCustomOptionsSetEnabled();
2359 customiseCheckbox.setToolTipText(
2360 MessageManager.getString("label.customise_description"));
2362 // customise checkbox
2365 presetsPanel.add(customiseCheckbox, gbc);
2367 // "Cancel changes" button (aligned with combo box above)
2369 presetsPanel.add(revertButton, gbc);
2371 return presetsPanel;
2374 private JPanel initBackupsTabFilenameExamplesPanel()
2376 String title = MessageManager
2377 .getString("label.scheme_examples");
2378 TitledBorder tb = new TitledBorder(title);
2379 exampleFilesPanel.setBorder(tb);
2380 exampleFilesPanel.setLayout(new GridBagLayout());
2383 backupfilesExampleLabel.setEditable(false);
2384 backupfilesExampleLabel
2385 .setBackground(exampleFilesPanel.getBackground());
2387 updateBackupFilesExampleLabel();
2389 GridBagConstraints gbc = new GridBagConstraints();
2392 gbc.fill = GridBagConstraints.NONE;
2393 gbc.anchor = GridBagConstraints.FIRST_LINE_START;
2395 exampleFilesPanel.add(backupfilesExampleLabel, gbc);
2396 return exampleFilesPanel;
2399 private void backupsTabUpdatePresets()
2401 IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
2404 String value = entry.v;
2406 if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
2410 BackupFilesPresetEntry.backupfilesPresetEntriesValues
2416 "Preset '" + value + "' [key:" + key + "] not implemented");
2419 // Custom options will now be enabled when the customiseCheckbox is checked
2420 // (performed above)
2421 // backupfilesCustomOptionsSetEnabled();
2422 updateBackupFilesExampleLabel();
2425 protected int getComboIntStringKey(
2426 JComboBox<Object> backupfilesPresetsCombo2)
2428 IntKeyStringValueEntry e;
2431 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
2433 } catch (Exception ex)
2436 "Problem casting Combo entry to IntKeyStringValueEntry.");
2439 return e != null ? e.k : 0;
2442 protected void setComboIntStringKey(
2443 JComboBox<Object> backupfilesPresetsCombo2,
2446 for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
2448 IntKeyStringValueEntry e;
2451 e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
2452 } catch (Exception ex)
2455 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
2460 backupfilesPresetsCombo2.setSelectedIndex(i);
2464 // backupsTabUpdatePresets();
2467 private JPanel initBackupsTabSuffixPanel()
2469 suffixPanel.setBorder(new TitledBorder(
2470 MessageManager.getString("label.backup_filename_strategy")));
2471 suffixPanel.setLayout(new GridBagLayout());
2474 .setText(MessageManager.getString("label.append_to_filename"));
2475 suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
2476 suffixTemplateLabel.setFont(LABEL_FONT);
2478 final String tooltip = JvSwingUtils.wrapTooltip(true,
2479 MessageManager.getString("label.append_to_filename_tooltip"));
2480 suffixTemplate.setToolTipText(tooltip);
2481 suffixTemplate.addActionListener(new ActionListener()
2484 public void actionPerformed(ActionEvent e)
2486 updateBackupFilesExampleLabel();
2487 backupfilesCustomOptionsSetEnabled();
2488 backupfilesRevertButtonSetEnabled(true);
2492 suffixTemplate.addKeyListener(new KeyListener()
2495 public void keyReleased(KeyEvent e)
2497 updateBackupFilesExampleLabel();
2498 backupfilesCustomOptionsSetEnabled();
2499 backupfilesRevertButtonSetEnabled(true);
2503 public void keyPressed(KeyEvent e)
2507 // disable use of ':' or '/' or '\'
2509 public void keyTyped(KeyEvent e)
2511 char c = e.getKeyChar();
2512 if (c == ':' || c == '/' || c == '\\')
2514 // don't process ':' or '/' or '\'
2523 .setText(MessageManager.getString("label.index_digits"));
2524 suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
2525 suffixDigitsLabel.setFont(LABEL_FONT);
2526 ChangeListener c = new ChangeListener()
2529 public void stateChanged(ChangeEvent e)
2531 backupfilesRevertButtonSetEnabled(true);
2532 updateBackupFilesExampleLabel();
2536 setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
2537 BackupFilesPresetEntry.DIGITSMAX, 3, c);
2539 suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
2540 MessageManager.getString("label.increment_index"));
2541 suffixReverse.addActionListener(new ActionListener()
2544 public void actionPerformed(ActionEvent e)
2546 boolean okay = true;
2547 if (warnAboutSuffixReverseChange())
2550 okay = confirmSuffixReverseChange();
2554 backupfilesRevertButtonSetEnabled(true);
2555 updateBackupFilesExampleLabel();
2559 boolean savedSuffixReverse = BackupFilesPresetEntry
2560 .getSavedBackupEntry().reverse;
2561 suffixReverse.setSelected(savedSuffixReverse);
2566 GridBagConstraints sgbc = new GridBagConstraints();
2568 // first row (template text box)
2569 sgbc.anchor = GridBagConstraints.WEST;
2573 sgbc.gridheight = 1;
2576 sgbc.fill = GridBagConstraints.NONE;
2577 suffixPanel.add(suffixTemplateLabel, sgbc);
2580 sgbc.fill = GridBagConstraints.HORIZONTAL;
2581 suffixPanel.add(suffixTemplate, sgbc);
2583 // second row (number of digits spinner)
2587 sgbc.fill = GridBagConstraints.NONE;
2588 suffixPanel.add(suffixDigitsLabel, sgbc);
2591 sgbc.fill = GridBagConstraints.HORIZONTAL;
2592 suffixPanel.add(suffixDigitsSpinner, sgbc);
2594 // third row (forward order radio selection)
2597 sgbc.gridwidth = GridBagConstraints.REMAINDER;
2598 sgbc.fill = GridBagConstraints.HORIZONTAL;
2599 suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
2601 // fourth row (reverse order radio selection)
2603 suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
2607 private boolean confirmSuffixReverseChange()
2609 boolean ret = false;
2610 String warningMessage = MessageManager
2611 .getString("label.warning_confirm_change_reverse");
2612 int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
2614 MessageManager.getString("label.change_increment_decrement"),
2615 JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
2617 ret = (confirm == JvOptionPane.YES_OPTION);
2621 private JPanel initBackupsTabKeepFilesPanel()
2623 keepfilesPanel.setBorder(
2624 new TitledBorder(MessageManager.getString("label.keep_files")));
2625 keepfilesPanel.setLayout(new GridBagLayout());
2627 backupfilesKeepAll.setLabels(
2628 MessageManager.getString("label.keep_all_backup_files"),
2629 MessageManager.getString(
2630 "label.keep_only_this_number_of_backup_files"));
2631 backupfilesKeepAll.addTrueActionListener(new ActionListener()
2634 public void actionPerformed(ActionEvent e)
2636 backupfilesRevertButtonSetEnabled(true);
2637 updateBackupFilesExampleLabel();
2640 backupfilesKeepAll.addActionListener(new ActionListener()
2643 public void actionPerformed(ActionEvent e)
2645 backupfilesRevertButtonSetEnabled(true);
2646 keepRollMaxOptionsEnabled();
2647 updateBackupFilesExampleLabel();
2651 ChangeListener c = new ChangeListener()
2654 public void stateChanged(ChangeEvent e)
2656 backupfilesRevertButtonSetEnabled(true);
2657 updateBackupFilesExampleLabel();
2661 setIntegerSpinner(backupfilesRollMaxSpinner,
2662 BackupFilesPresetEntry.ROLLMAXMIN,
2663 BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
2665 backupfilesConfirmDelete.setLabels(
2666 MessageManager.getString("label.always_ask"),
2667 MessageManager.getString("label.auto_delete"));
2668 backupfilesConfirmDelete.addActionListener(new ActionListener()
2671 public void actionPerformed(ActionEvent e)
2673 backupfilesRevertButtonSetEnabled(true);
2676 // update the enabled section
2677 keepRollMaxOptionsEnabled();
2679 GridBagConstraints kgbc = new GridBagConstraints();
2681 // first row (template text box)
2682 kgbc.anchor = GridBagConstraints.WEST;
2685 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2686 kgbc.gridheight = 1;
2689 kgbc.fill = GridBagConstraints.HORIZONTAL;
2690 keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
2696 kgbc.gridwidth = GridBagConstraints.RELATIVE;
2697 keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
2700 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2701 keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
2703 // third row (indented)
2705 kgbc.insets = new Insets(0, 20, 0, 0);
2708 kgbc.gridwidth = GridBagConstraints.REMAINDER;
2709 kgbc.fill = GridBagConstraints.HORIZONTAL;
2712 JPanel jp = new JPanel();
2713 jp.setLayout(new FlowLayout());
2715 .setText(MessageManager
2716 .getString("label.autodelete_old_backup_files"));
2717 oldBackupFilesLabel.setFont(LABEL_FONT);
2718 oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
2719 jp.add(oldBackupFilesLabel);
2720 jp.add(backupfilesConfirmDelete.getTrueButton());
2721 jp.add(backupfilesConfirmDelete.getFalseButton());
2722 keepfilesPanel.add(jp, kgbc);
2724 return keepfilesPanel;
2727 protected void updateBackupFilesExampleLabel()
2729 int exampleindex = 12;
2730 String base = MessageManager.getString("label.filename") + ".fa";
2731 if (base == null || base.length() == 0)
2733 base = "file_name.fa";
2736 boolean reverse = suffixReverse.isSelected();
2737 boolean keepAll = backupfilesKeepAll.isSelected();
2739 String suffix = suffixTemplate.getText();
2742 backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
2743 if (suffix == null || suffix.length() == 0)
2745 backupfilesExampleLabel
2746 .setText(MessageManager.getString("label.no_backup_files"));
2747 backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
2751 rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
2752 rollMax = rollMax < 1 ? 1 : rollMax;
2754 if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
2759 digits = getSpinnerInt(suffixDigitsSpinner, 3);
2760 digits = digits < 1 ? 1 : digits;
2762 int lowersurround = 2;
2763 int uppersurround = 0;
2764 StringBuilder exampleSB = new StringBuilder();
2765 boolean firstLine = true;
2771 int max = keepAll ? exampleindex : rollMax;
2772 for (int index = min; index <= max; index++)
2774 if (index == min + lowersurround && index < max - uppersurround - 1)
2776 exampleSB.append("\n...");
2779 else if (index > min + lowersurround && index < max - uppersurround)
2791 exampleSB.append("\n");
2794 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2795 base, suffix, digits));
2798 // no extra text needed
2800 else if (index == min)
2802 String newest = MessageManager.getString("label.braced_newest");
2803 if (newest != null && newest.length() > 0)
2805 exampleSB.append(" " + newest);
2808 else if (index == max)
2810 String oldest = MessageManager.getString("label.braced_oldest");
2811 if (oldest != null && oldest.length() > 0)
2813 exampleSB.append(" " + oldest);
2822 int min = (keepAll || exampleindex - rollMax < 0) ? 1
2823 : exampleindex - rollMax + 1;
2824 int max = exampleindex;
2826 for (int index = min; index <= max; index++)
2829 if (index == min + lowersurround && index < max - uppersurround - 1)
2831 exampleSB.append("\n...");
2834 else if (index > min + lowersurround && index < max - uppersurround)
2846 exampleSB.append("\n");
2849 exampleSB.append(BackupFilenameParts.getBackupFilename(index,
2850 base, suffix, digits));
2853 // no extra text needed
2855 else if (index == min)
2857 String oldest = MessageManager.getString("label.braced_oldest");
2858 if (oldest != null && oldest.length() > 0)
2860 exampleSB.append(" " + oldest);
2863 else if (index == max)
2865 String newest = MessageManager.getString("label.braced_newest");
2866 if (newest != null && newest.length() > 0)
2868 exampleSB.append(" " + newest);
2876 // add some extra empty lines to pad out the example files box. ugh, please tell
2877 // me how to do this better
2878 int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
2879 if (remainingLines > 0)
2881 for (int i = 0; i < remainingLines; i++)
2883 exampleSB.append("\n ");
2888 backupfilesExampleLabel.setText(exampleSB.toString());
2891 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2892 boolean useExistingVal, ChangeListener c)
2899 i = ((Integer) s.getValue()).intValue();
2900 } catch (Exception e)
2903 "Exception casting the initial value of s.getValue()");
2907 setIntegerSpinner(s, min, max, i, c);
2910 protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
2913 // integer spinner for number of digits
2922 SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
2925 s.addChangeListener(c);
2929 protected static int getSpinnerInt(JSpinner s, int def)
2935 i = (Integer) s.getValue();
2936 } catch (Exception e)
2938 Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
2943 private void keepRollMaxOptionsEnabled()
2945 boolean enabled = backupfilesKeepAll.isEnabled()
2946 && !backupfilesKeepAll.isSelected();
2947 oldBackupFilesLabel.setEnabled(enabled);
2948 backupfilesRollMaxSpinner.setEnabled(enabled);
2949 backupfilesConfirmDelete.setEnabled(enabled);
2952 private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
2954 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2955 && customiseCheckbox.isSelected()
2956 && suffixTemplate.getText()
2957 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2958 keepfilesPanel.setEnabled(enabled);
2959 backupfilesKeepAll.setEnabled(enabled);
2960 oldBackupFilesLabel.setEnabled(enabled);
2961 keepRollMaxOptionsEnabled();
2964 private void backupfilesSuffixTemplateDigitsSetEnabled()
2966 boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
2967 .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
2968 suffixDigitsLabel.setEnabled(enabled);
2969 suffixDigitsSpinner.setEnabled(enabled);
2970 suffixReverse.setEnabled(enabled);
2973 private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
2975 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2976 && customiseCheckbox.isSelected();
2977 suffixPanel.setEnabled(enabled);
2978 suffixTemplateLabel.setEnabled(enabled);
2979 suffixTemplate.setEnabled(enabled);
2980 backupfilesSuffixTemplateDigitsSetEnabled();
2983 private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
2985 boolean enabled = tryEnabled && enableBackupFiles.isSelected()
2986 && customiseCheckbox.isSelected() && backupfilesCustomChanged();
2987 revertButton.setEnabled(enabled);
2990 private boolean backupfilesCustomChanged()
2992 BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
2993 .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
2994 BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
2995 return !custom.equals(current);
2998 protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
3000 String suffix = suffixTemplate.getText();
3001 int digits = getSpinnerInt(suffixDigitsSpinner, 3);
3002 boolean reverse = suffixReverse.isSelected();
3003 boolean keepAll = backupfilesKeepAll.isSelected();
3004 int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
3005 boolean confirmDelete = backupfilesConfirmDelete.isSelected();
3007 BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
3008 reverse, keepAll, rollMax, confirmDelete);
3013 protected void backupfilesCustomOptionsSetEnabled()
3015 boolean enabled = customiseCheckbox.isSelected();
3017 backupfilesRevertButtonSetEnabled(enabled);
3018 backupfilesSuffixTemplateSetEnabled(enabled);
3019 backupfilesKeepAllSetEnabled(enabled);
3022 private void backupfilesSummarySetEnabled()
3024 boolean enabled = enableBackupFiles.isSelected();
3025 backupfilesExampleLabel.setEnabled(enabled);
3026 exampleFilesPanel.setEnabled(enabled);
3029 private void backupfilesPresetsSetEnabled()
3031 boolean enabled = enableBackupFiles.isSelected();
3032 presetsPanel.setEnabled(enabled);
3033 presetsComboLabel.setEnabled(enabled);
3034 backupfilesPresetsCombo.setEnabled(enabled);
3035 customiseCheckbox.setEnabled(enabled);
3036 revertButton.setEnabled(enabled);
3039 protected void backupsOptionsSetEnabled()
3041 backupfilesPresetsSetEnabled();
3042 backupfilesSummarySetEnabled();
3043 backupfilesCustomOptionsSetEnabled();
3046 protected void backupsSetOptions(String suffix, int digits,
3047 boolean reverse, boolean keepAll, int rollMax,
3048 boolean confirmDelete)
3050 suffixTemplate.setText(suffix);
3051 suffixDigitsSpinner.setValue(digits);
3052 suffixReverse.setSelected(reverse);
3053 backupfilesKeepAll.setSelected(keepAll);
3054 backupfilesRollMaxSpinner.setValue(rollMax);
3055 backupfilesConfirmDelete.setSelected(confirmDelete);
3058 protected void backupsSetOptions(BackupFilesPresetEntry p)
3060 backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
3064 protected void autoIdWidth_actionPerformed()
3066 // TODO Auto-generated method stub
3070 protected void userIdWidth_actionPerformed()
3072 // TODO Auto-generated method stub
3076 protected void maxColour_actionPerformed(JPanel panel)
3080 protected void minColour_actionPerformed(JPanel panel)
3084 protected void gapColour_actionPerformed(JPanel panel)
3088 protected void hiddenColour_actionPerformed(JPanel panel)
3092 protected void showunconserved_actionPerformed(ActionEvent e)
3094 // TODO Auto-generated method stub
3098 protected void useLegacyGaps_actionPerformed(ActionEvent e)
3102 protected void resetOvDefaults_actionPerformed(ActionEvent e)
3112 public void ok_actionPerformed(ActionEvent e)
3122 public void cancel_actionPerformed(ActionEvent e)
3132 public void annotations_actionPerformed(ActionEvent e)
3139 public void startupFileTextfield_mouseClicked()
3143 public void newLink_actionPerformed(ActionEvent e)
3148 public void editLink_actionPerformed(ActionEvent e)
3153 public void deleteLink_actionPerformed(ActionEvent e)
3158 public void defaultBrowser_mouseClicked(MouseEvent e)
3163 public void linkURLList_keyTyped(KeyEvent e)
3168 public void setProxyAuthEnabled()
3170 boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
3171 proxyAuthUsernameLabel.setEnabled(enabled);
3172 proxyAuthPasswordLabel.setEnabled(enabled);
3173 passwordNotStoredLabel.setEnabled(enabled);
3174 proxyAuthUsernameTB.setEnabled(enabled);
3175 proxyAuthPasswordPB.setEnabled(enabled);
3178 public void setCustomProxyEnabled()
3180 boolean enabled = customProxy.isSelected();
3181 portLabel.setEnabled(enabled);
3182 serverLabel.setEnabled(enabled);
3183 portLabel2.setEnabled(enabled);
3184 serverLabel2.setEnabled(enabled);
3185 httpLabel.setEnabled(enabled);
3186 httpsLabel.setEnabled(enabled);
3187 proxyServerHttpTB.setEnabled(enabled);
3188 proxyPortHttpTB.setEnabled(enabled);
3189 proxyServerHttpsTB.setEnabled(enabled);
3190 proxyPortHttpsTB.setEnabled(enabled);
3191 proxyAuth.setEnabled(enabled);
3192 setProxyAuthEnabled();
3195 public void proxyType_actionPerformed()
3197 setCustomProxyEnabled();
3198 proxyAuthPasswordHighlight(true);
3201 public void proxyAuth_actionPerformed()
3203 setProxyAuthEnabled();
3204 proxyAuthPasswordHighlight(true);
3208 * Customer renderer for JTable: supports column of radio buttons
3210 public class RadioButtonRenderer extends JRadioButton
3211 implements TableCellRenderer
3213 public RadioButtonRenderer()
3215 setHorizontalAlignment(CENTER);
3216 setToolTipText(MessageManager.getString("label.urltooltip"));
3220 public Component getTableCellRendererComponent(JTable table,
3221 Object value, boolean isSelected, boolean hasFocus, int row,
3224 setSelected((boolean) value);
3226 // set colours to match rest of table
3229 setBackground(table.getSelectionBackground());
3230 setForeground(table.getSelectionForeground());
3234 setBackground(table.getBackground());
3235 setForeground(table.getForeground());
3242 * Customer cell editor for JTable: supports column of radio buttons in
3243 * conjunction with renderer
3245 public class RadioButtonEditor extends AbstractCellEditor
3246 implements TableCellEditor
3248 private JRadioButton button = new JRadioButton();
3250 public RadioButtonEditor()
3252 button.setHorizontalAlignment(SwingConstants.CENTER);
3253 this.button.addActionListener(new ActionListener()
3256 public void actionPerformed(ActionEvent e)
3258 fireEditingStopped();
3264 public Component getTableCellEditorComponent(JTable table, Object value,
3265 boolean isSelected, int row, int column)
3267 button.setSelected((boolean) value);
3272 public Object getCellEditorValue()
3274 return button.isSelected();